US20080032299A1 - Methods for prognosis and treatment of solid tumors - Google Patents

Methods for prognosis and treatment of solid tumors Download PDF

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US20080032299A1
US20080032299A1 US11/715,606 US71560607A US2008032299A1 US 20080032299 A1 US20080032299 A1 US 20080032299A1 US 71560607 A US71560607 A US 71560607A US 2008032299 A1 US2008032299 A1 US 2008032299A1
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gene
class
genes
prognosis
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Michael Burczynski
Natalie Twine
William Trepicchio
Andrew Strahs
Fred Immermann
Donna Slonim
Andrew Dorner
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Wyeth LLC
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G01N33/57438—Specifically defined cancers of liver, pancreas or kidney
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57484—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
    • G01N33/57496—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites involving intracellular compounds
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/118—Prognosis of disease development
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Definitions

  • Each compact disc includes the following files: “Sequence Listing.ST25.txt” (5,454 KB, created Mar. 8, 2007), “Table 3—Spearman Correlation of Baseline Expression with Clinical Outcome.txt” (298 KB, created Jan. 19, 2004), “Table 4—Qualifiers and the Corresponding Entrez and Unigene Accession Nos.txt” (179 KB, created Jan. 20, 2004), “Table 5—Genes and Gene Titles.txt” (331 KB, created Jan.
  • the present invention relates to solid tumor prognosis genes and methods of using these genes for the prognosis or treatment of solid tumors.
  • the present invention provides methods, systems and equipment for prognosis or selection of treatment of solid tumors.
  • Prognosis genes for a solid tumor can be identified by the present invention.
  • the expression profiles of these genes in peripheral blood mononuclear cells (PBMCs) are correlated with clinical outcome of the solid tumor.
  • PBMCs peripheral blood mononuclear cells
  • These genes can be used as surrogate markers for predicting clinical outcome of the solid tumor in a patient of interest.
  • These genes can also be used to identify or select treatments which have favorable prognoses for the patient of interest.
  • the present invention provides methods that are useful for the prognosis or selection of treatment of a solid tumor in a patient of interest.
  • the methods include comparing an expression profile of one or more prognosis genes in a peripheral blood sample of the patient of interest to at least one reference expression profile of the prognosis genes.
  • Each of the prognosis genes is differentially expressed in PBMCs of a first class of patients as compared to PBMCs of a second class of patients. Both classes of patients have a solid tumor, and each class of patients has a different clinical outcome.
  • the prognosis genes are substantially correlated with a class distinction between the two classes of patients.
  • Solid tumors amenable to the present invention include, but are not limited to, renal cell carcinoma (RCC), prostate cancer, head/neck cancer, and other tumors that do not have their origin in blood or lymph cells.
  • RRC renal cell carcinoma
  • prostate cancer prostate cancer
  • head/neck cancer head/neck cancer
  • other tumors that do not have their origin in blood or lymph cells include, but are not limited to, renal cell carcinoma (RCC), prostate cancer, head/neck cancer, and other tumors that do not have their origin in blood or lymph cells.
  • Clinical outcome can be measured by any clinical indicator.
  • clinical outcome is determined based on clinical classifications such as complete response, partial response, minor response, stable disease, progressive disease, non-progressive disease, or any combination thereof.
  • clinical outcome is measured by time to disease progression (TTP) or time to death (TTD).
  • clinical outcome is prognosticated by using traditional risk assessment methods, such as Motzer risk classification for RCC.
  • Other patient responses to a therapeutic treatment can also be used to measure clinical outcome. Examples of solid tumor treatments include, but are not limited to, drug therapy (e.g., CCI-779 therapy), chemotherapy, hormone therapy, radiotherapy, immunotherapy, surgery, gene therapy, anti-angiogenesis therapy, palliative therapy, or any combination thereof.
  • the reference expression profile(s) includes an average expression profile of the prognosis genes in peripheral blood samples of reference patients.
  • the reference patients have the same solid tumor as the patient of interest, and the clinical outcome of the reference patients are either known or determinable.
  • peripheral blood samples of the patient of interest and reference patients can be whole blood samples, or blood samples comprising enriched or purified PBMCs. Other types of blood samples can also be employed in the present invention. In one embodiment, all of the peripheral blood samples are baseline samples which are isolated from respective patients prior to a therapeutic treatment of the patients.
  • any comparison method can be used to compare the expression profile of the patient of interest to the reference expression profile(s).
  • the comparison is based on the absolute or relative peripheral blood expression level of each prognosis gene.
  • the comparison is based on the ratios between expression levels of two or more prognosis genes.
  • the reference expression profiles include at least two distinct expression profiles, each being derived from a different class of reference patients. The comparison of the expression profile of the patient of interest to the reference expression profiles can be carried out by using methods including, but not limited to, hierarchical clustering, k-nearest-neighbors, or weighted-voting algorithm.
  • the methods of the present invention include selecting a treatment which has a favorable prognosis for the solid tumor in the patient of interest.
  • the present invention provides other methods useful for the prognosis or selection of treatment of a solid tumor in a patient of interest. These methods include comparing an expression profile of one or more prognosis genes in a peripheral blood sample of the patient of interest to at least one reference expression profile of the prognosis genes, where each of the prognosis genes is differentially expressed in PBMCs of a first class of patients as compared to PBMCs of a second class of patients.
  • Each of the first and second classes is a subcluster formed by an unsupervised clustering analysis of gene expression profiles in PBMCs of patients who have the solid tumor.
  • the majority of the first class of patients has a first clinical outcome
  • the majority of the second class of patients has a second clinical outcome.
  • the present invention further provides methods useful for the prognosis or selection of treatment of a solid tumor in a patient of interest.
  • the methods include comparing an expression profile of one or more prognosis genes in a peripheral blood sample of the patient of interest to at least one reference expression profile of the prognosis genes, where the expression levels of each of the prognosis genes in PBMCs of patients having the solid tumor are correlated with clinical outcomes of these patients.
  • the association between PBMC expression levels and clinical outcome can be determined by a statistical method (e.g., Spearman's rank correlation or Cox proportional hazard regression model) or a class-based correlation metric (e.g., neighborhood analysis).
  • the solid tumor is RCC
  • clinical outcome is measured by patient response to a CCI-779 therapy.
  • the prognosis genes include at least one gene selected from Tables 6a, 6b, 6c, 6d, 9a, 9b, 9c, 9d, 10, 11, 12, 13, 16, 20, and 21.
  • the present invention also features systems useful for the prognosis or selection of treatment of a solid tumor in a patient of interest.
  • the systems include (1) a memory or a storage medium comprising data that represent an expression profile of one or more prognosis genes in a peripheral blood sample of the patient of interest, (2) a storage medium comprising data that represent at least one reference expression profile of the prognosis genes, (3) a program capable of comparing the expression profile of the patient of interest to the reference expression profile, and (4) a processor capable of executing the program.
  • the expression levels of the prognosis genes in PBMCs of patients having the solid tumor are correlated with clinical outcomes of the patients.
  • the present invention features nucleic acid or protein arrays useful for the prognosis or selection of treatment of a solid tumor in a patient of interest.
  • the nucleic acid or protein arrays include concentrated probes for solid tumor prognosis genes.
  • FIG. 1A depicts expression profiles of class-correlated genes identified by nearest-neighbor analysis of patients with survival of less than 150 days versus patients with survival of greater than 550 days.
  • the relative expression levels of the class-correlated genes are indicated for each patient (columns) according to the normalized expression level scale.
  • FIG. 1B shows the comparison of the signal to noise (S2N) similarity metric scores for class-correlated genes identified in FIG. 1A relative to S2N scores for the top 1%, 5%, and 50% of scores for class-correlated genes resulting from randomly permuted data sets.
  • S2N signal to noise
  • FIG. 1C illustrates training set cross validation results for predictor gene sets of increasing size. Each predictor set was evaluated by cross validation to identify the predictor set with the highest accuracy for classification of the samples. In these analyses, a 58 gene predictor set (77% accuracy) was the optimal classifier.
  • FIG. 1D demonstrates cross validation results for each sample using the 58-gene predictor identified in FIG. 1C .
  • a leave-one-out cross validation was performed and the prediction strengths were calculated for each sample in the analysis.
  • confidence scores accompanying calls of “TTD>550 days” were assigned positive values, while prediction strengths accompanying calls of “TTD ⁇ 150 days” were assigned negative values.
  • FIG. 2A shows the relative gene expression levels of a 42-gene classifier for the comparison of patients with intermediate versus poor Motzer risk classification.
  • FIG. 2B shows the relative gene expression levels for an 18-gene classifier identified in the comparison of patients with progressive disease versus any other clinical response.
  • FIG. 2C demonstrates the relative gene expression levels for a 6-gene classifier identified in the comparison of patients in the lower versus upper quartiles of time to disease progression.
  • FIG. 2D shows the relative gene expression levels for a 52-gene classifier identified in the comparison of patients in the lower versus upper quartiles of survival/time to death.
  • FIG. 2E depicts the relative expression levels for a 12-gene classifier identified in the comparison of patients with early (time to disease progression ⁇ 106 days) versus all other times to disease progression (TTP ⁇ 106 days).
  • FIG. 3A illustrates the dendrogram of an unsupervised hierarchical clustering of baseline PBMC profiles in 45 RCC patients using all expressed genes present in at least one sample and possessing a frequency of greater than 10 ppm in at least one sample (5,424 genes total).
  • PBMC expression profiles in the poor prognosis cluster are indicated by subcluster “A,” where 9 out of 12 patients with PBMC profiles in this subcluster exhibited survival of less than a year.
  • PBMC expression profiles in the good prognosis cluster are indicated by subcluster “C,” where 10 out of 12 patients with PBMC profiles in this subcluster exhibited survival of greater than a year.
  • the median survival for patients in subclusters A, B, C, and D is 281 days, 566 days, 573 days, and 502 days, respectively.
  • FIG. 3B shows baseline expression profiles of selected genes in RCC patients. The dendrogram of sample relatedness is indicated.
  • FIG. 4A illustrates the Kaplan-Meier survival curve for patients in the poor and good prognosis subclusters segregated on the basis of gene expression pattern.
  • FIG. 4B illustrates the Kaplan-Meier survival curve for patients in the poor and good prognosis subclusters segregated on the basis of Motzer risk assessment.
  • FIG. 5A demonstrates the result of supervised identification of a gene classifier for assigning class membership to patients in the good and poor prognosis subclusters.
  • the relative expression levels of the most class-correlated gene (rows) are indicated for each patient (columns) according to the scale described in FIG. 1A .
  • FIG. 5B shows cross validation results for each sample using the gene classifier of FIG. 5A .
  • a leave-one-out cross validation was performed and the confidence scores were calculated for each sample in the analysis. Similar to FIG. 1D , for the purposes of illustration, prediction strengths accompanying calls of “survival>1 year” were assigned positive values, while prediction strengths accompanying calls of “survival ⁇ 1 year” were assigned negative values. Asterisks identify the false positives in this clinical assay designed to identify short survival times, and arrowheads indicate false negatives.
  • FIG. 6A shows the optimal gene classifier for year-long survival identified by nearest-neighbor analysis using a more stringent filter (at least 25% present calls, and an average frequency no less than 5 ppm).
  • a GeneCluster gene selection approach identifies genes distinguishing patients with survival less than 365 days versus patients with survival greater than 365 days in the training set. The relative expression levels of the most class-correlated genes (rows) are indicated for each of the patients in the training set (columns) according to the scale described in FIG. 1A .
  • FIG. 6B evaluates prediction accuracy of gene classifiers of increasing size. Accuracy of class assignment for gene classifiers containing between 2 and 60 genes in steps of 2, and 60-200 genes in steps of 10, were evaluated by leave-one-out cross validation on the training set of samples. The smallest predictive model with the highest accuracy was selected (20 gene predictor, indicated by the arrow).
  • FIG. 6C demonstrates the result of evaluation of the optimal predictive model of FIG. 6B on an untested set of RCC PBMC profiles.
  • a k-nearest-neighbors algorithm using the 20 gene classifier was used to assign class membership to the remaining 14 PBMC profiles, and the prediction strengths associated with the class assignments are presented for each sample in the analysis.
  • confidence scores accompanying calls of “TTD ⁇ 365 days” were assigned positive values, while confidence scores accompanying calls of “TTD>365 days” were assigned negative values.
  • the overall accuracy of the gene classifier was 72%.
  • FIG. 7A illustrates the optimal gene classifier for greater than 106 day time to progression identified by nearest-neighbor analysis using a more stringent filter (at least 25% present calls, and an average frequency no less than 5 ppm).
  • a GeneCluster gene selection approach identifies genes distinguishing patients with TTP less than 106 days versus patients with TTP greater than 106 days in the training set. The relative expression levels of the most class-correlated genes (rows) are indicated for each of the patients in the training set (columns) according to the scale of FIG. 1A .
  • FIG. 7B indicates prediction accuracy of gene classifiers of increasing size. Accuracy of class assignment for gene classifiers containing between 2 and 60 genes in steps of 2, and 60-200 genes in steps of 10, were evaluated by leave-one-out cross validation on the training set of samples. The smallest predictive model with the highest accuracy was selected (30 gene predictor, indicated by the arrow).
  • FIG. 7C shows the result of evaluation of the optimal predictive model of FIG. 7B on an untested set of RCC PBMC profiles.
  • a k-nearest-neighbors algorithm using the 30 gene classifier was used to assign class membership to the remaining 14 PBMC profiles, and the prediction strengths associated with the class assignments are presented for each sample in the analysis.
  • confidence scores accompanying calls of “TTP ⁇ 106 days” were assigned positive values, while confidence scores accompanying calls of “TTD>106 days” were assigned negative values.
  • the overall accuracy of the gene classifier was 85%.
  • the present invention provides methods that are useful for prognosis or selection of treatment of solid tumors. These methods employ prognosis genes that are differentially expressed in peripheral blood samples of solid tumor patients who have different clinical outcomes.
  • the peripheral blood expression profiles of these prognosis genes are correlated with patients' clinical outcome or prognosis under a statistical method or a correlation model.
  • solid tumor patients can be divided into at least two classes based on patients' clinical outcome or prognosis, and the prognosis genes are substantially correlated with a class distinction between these two classes of patients under a neighborhood analysis.
  • the prognosis genes of the present invention can be used as surrogate markers for the prediction of clinical outcome of solid tumors.
  • the prognosis genes of the present invention can also be used for the identification of optimal treatments of solid tumors. Different patients may have distinct clinical responses to a therapeutic treatment due to individual heterogeneity of the molecular mechanism of the disease.
  • the identification of gene expression patterns that correlate with patient response allows clinicians to select treatments based on predicted patient responses and thereby avoid adverse reactions. This provides improved power and safety of clinical trials and increased benefit/risk ratio for drugs and other therapeutic treatments.
  • Peripheral blood is a tissue that can be routinely obtained from patients in a minimally invasive manner. By determining the correlation between patient outcome and gene expression profiles in peripheral blood samples, the present invention represents a significant advance in clinical pharmacogenomics and solid tumor treatment.
  • the present invention further evaluates the correlation between peripheral blood gene expression and clinical outcome of solid tumors.
  • Prognosis genes for a variety of solid tumors can be identified by the present invention. These genes are differentially expressed in peripheral blood samples of solid tumor patients who have different clinical outcomes.
  • the peripheral blood expression profiles of the prognosis genes of the present invention are correlated with patient outcome under statistical methods or correlation models. Exemplary statistical methods and correlation models include, but are not limited to, Spearman's rank correlation, Cox proportional hazard regression model, ANOVA/t test, nearest-neighbor analysis, and other rank tests, survival models or class-based correlation metrics.
  • Solid tumors amenable to the present invention include, without limitation, RCC, prostate cancer, head/neck cancer, ovarian cancer, testicular cancer, brain tumor, breast cancer, lung cancer, colon cancer, pancreas cancer, stomach cancer, bladder cancer, skin cancer, cervical cancer, uterine cancer, and liver cancer.
  • the solid tumors do not have their origin in blood or lymph (hematopoetic) cells. Solid tumors can be measured or evaluated using direct or indirect visualization procedures.
  • Suitable visualization methods include, but are not limited to, scans (such as X-rays, computerized axial tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), or ultrasonography (U/S)), biopsy, palpation, endoscopy, laparoscopy, and other suitable means as appreciated by those skilled in the art.
  • scans such as X-rays, computerized axial tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), or ultrasonography (U/S)
  • CT computerized axial tomography
  • MRI magnetic resonance imaging
  • PET positron emission tomography
  • U/S ultrasonography
  • Clinical outcome of solid tumors can be assessed by numerous criteria. In many embodiments, clinical outcome is assessed based on patients' response to a therapeutic treatment. Examples of clinical outcome measures include, without limitation, complete response, partial response, minor response, stable disease, progressive disease, time to disease progression (TTP), time to death (TTD or Survival), or any combination thereof. Examples of solid tumor treatments include, without limitation, drug therapy (e.g., CCI-779 therapy), chemotherapy, hormone therapy, radiotherapy, immunotherapy, surgery, gene therapy, anti-angiogenesis therapy, palliative therapy, or any combination thereof, or other conventional or non-conventional therapies.
  • drug therapy e.g., CCI-779 therapy
  • chemotherapy e.g., CCI-779 therapy
  • hormone therapy e.g., radiotherapy
  • immunotherapy e.g., surgery, gene therapy, anti-angiogenesis therapy, palliative therapy, or any combination thereof, or other conventional or non-conventional therapies.
  • clinical outcome is evaluated based on the WHO Reporting Criteria, such as those described in WHO Publication, No. 48 (World Health Organization, Geneva, Switzerland, 1979). Under the Criteria, uni- or bidimensionally measurable lesions are measured at each assessment. When multiple lesions are present in any organ, up to 6 representative lesions can be selected, if available.
  • clinical outcome is determined based on a classification system composed of clinical categories such as complete response, partial response, minor response, stable disease, progressive disease, or any combination thereof.
  • “Complete response” (CR) means complete disappearance of all measurable and evaluable disease, determined by two observations not less than 4 weeks apart. There is no new lesion and no disease related symptom.
  • “Partial response” (PR) in reference to bidimensionally measurable disease means decrease by at least about 50% of the sum of the products of the largest perpendicular diameters of all measurable lesions as determined by 2 observations not less than 4 weeks apart.
  • Partial response in reference to unidimensionally measurable disease means decrease by at least about 50% in the sum of the largest diameters of all lesions as determined by 2 observations not less than 4 weeks apart.
  • Minor response in reference to bidimensionally measurable disease means about 25% or greater decrease but less than about 50% decrease in the sum of the products of the largest perpendicular diameters of all measurable lesions. “Minor response” in reference to unidimensionally measurable disease means decrease by at least about 25% but less than about 50% in the sum of the largest diameters of all lesions.
  • “Stable disease” (SD) in reference to bidimensionally measurable disease means less than about 25% decrease or less than about 25% increase in the sum of the products of the largest perpendicular diameters of all measurable lesions. “Stable disease” in reference to unidimensionally measurable disease means less than about 25% decrease or less than about 25% increase in the sum of the diameters of all lesions. No new lesions should appear. “Progressive disease” (PD) refers to a greater than or equal to about a 25% increase in the size of at least one bidimensionally (product of the largest perpendicular diameters) or unidimensionally measurable lesion or appearance of a new lesion. The occurrence of pleural effusion or ascites is also considered as progressive disease if this is substantiated by positive cytology. Pathological fracture or collapse of bone is not necessarily evidence of disease progression.
  • overall subject tumor response for uni- and bidimensionally measurable disease is determined according to Table 1.
  • Table 1 Overall Subject Tumor Response Response in Response in Bidimensionally Unidimensionally Overall Subject Measurable Disease Measurable Disease Tumor Response PD Any PD Any PD PD SD SD or PR SD SD SD CR PR PR SD or PR or CR PR CR SD or PR PR CR CR CR
  • Clinical outcome can also be assessed by other criteria.
  • clinical outcome can be measured by TTP or TTD.
  • TTP refers to the interval from the date of initiation of a therapeutic treatment until the first day of measurement of progressive disease.
  • TTD refers to the interval from the date of initiation of a therapeutic treatment to the time of death, or censored at the last date known alive.
  • clinical outcome can include prognoses based on traditional clinical risk assessment methods.
  • these risk assessment methods employ numerous prognostic factors to classify patients into different prognosis or risk groups.
  • Motzer risk assessment for RCC as described in Motzer, et al., J C LIN O NCOL, 17:2530-2540 (1999). Patients in different risk groups may have different responses to a therapy.
  • Peripheral blood samples employed in the present invention can be isolated from solid tumor patients at any disease or treatment stage.
  • the peripheral blood samples are isolated from solid tumor patients prior to a therapeutic treatment. These blood samples are “baseline samples” with respect to the therapeutic treatment.
  • peripheral blood samples can be used in the present invention.
  • the peripheral blood samples are whole blood samples.
  • the peripheral blood samples comprise enriched PBMCs.
  • enriched it means that the percentage of PBMCs in the sample is higher than that in whole blood.
  • the PBMC percentage in an enriched sample is at least 1, 2, 3, 4, 5 or more times higher than that in whole blood.
  • the PBMC percentage in an enriched sample is at least 90%, 95%, 98%, 99%, 99.5%, or more.
  • Blood samples containing enriched PBMCs can be prepared using any method known in the art, such as Ficoll gradients centrifugation or CPTs (cell purification tubes).
  • peripheral blood gene expression profiles and patient outcome can be evaluated using global gene expression analyses.
  • Methods suitable for this purpose include, but are not limited to, nucleic acid arrays (such as cDNA or oligonucleotide arrays), 2-dimensional SDS-polyacrylamide gel electrophoresis/mass spectrometry, and other high throughput nucleotide or polypeptide detection techniques.
  • Nucleic acid arrays allow for quantitative detection of the expression levels of a large number of genes at one time.
  • Examples of nucleic acid arrays include, but are not limited to, Genechip® microarrays from Affymetrix (Santa Clara, Calif.), cDNA microarrays from Agilent Technologies (Palo Alto, Calif.), and bead arrays described in U.S. Pat. Nos. 6,288,220 and 6,391,562.
  • the polynucleotides to be hybridized to nucleic acid arrays can be labeled with one or more labeling moieties to allow for detection of hybridized polynucleotide complexes.
  • the labeling moieties can include compositions that are detectable by spectroscopic, photochemical, biochemical, bioelectronic, immunochemical, electrical, optical or chemical means.
  • Exemplary labeling moieties include radioisotopes, chemiluminescent compounds, labeled binding proteins, heavy metal atoms, spectroscopic markers such as fluorescent markers and dyes, magnetic labels, linked enzymes, mass spectrometry tags, spin labels, electron transfer donors and acceptors, and the like.
  • Unlabeled polynucleotides can also be employed.
  • the polynucleotides can be DNA, RNA, or a modified form thereof.
  • Hybridization reactions can be performed in absolute or differential hybridization formats.
  • absolute hybridization format polynucleotides derived from one sample, such as PBMCs from a patient in a selected outcome class, are hybridized to the probes on a nucleic acid array. Signals detected after the formation of hybridization complexes correlate to the polynucleotide levels in the sample.
  • differential hybridization format polynucleotides derived from two biological samples, such as one from a patient in a first outcome class and the other from a patient in a second outcome class, are labeled with different labeling moieties. A mixture of these differently labeled polynucleotides is added to a nucleic acid array.
  • the nucleic acid array is then examined under conditions in which the emissions from the two different labels are individually detectable.
  • the fluorophores Cy3 and Cy5 are used as the labeling moieties for the differential hybridization format.
  • nucleic acid array expression signals are scaled or normalized before being subject to further analysis. For instance, the expression signals for each gene can be normalized to take into account variations in hybridization intensities when more than one array is used under similar test conditions. Signals for individual polynucleotide complex hybridization can also be normalized using the intensities derived from internal normalization controls contained on each array. In addition, genes with relatively consistent expression levels across the samples can be used to normalize the expression levels of other genes.
  • the expression levels of the genes are normalized across the samples such that the mean is zero and the standard deviation is one.
  • the expression data detected by nucleic acid arrays are subject to a variation filter which excludes genes showing minimal or insignificant variation across all samples.
  • the gene expression data collected from nucleic acid arrays can be correlated with clinical outcome using a variety of methods. Suitable correlation methods include, but are not limited to, statistical methods (such as Spearman's rank correlation, Cox proportional hazard regression model, ANOVA/t test, or other suitable rank tests or survival models) and class-based correlation metrics (such as nearest-neighbor analysis).
  • statistical methods such as Spearman's rank correlation, Cox proportional hazard regression model, ANOVA/t test, or other suitable rank tests or survival models
  • class-based correlation metrics such as nearest-neighbor analysis
  • class-based correlation metrics are used to identify the correlation between peripheral blood gene expression and clinical outcome.
  • patients with a specified solid tumor are divided into at least two classes based on their clinical stratifications.
  • the correlation between peripheral blood gene expression (e.g., in PBMCs) and clinical outcome is analyzed by a supervised cluster algorithm.
  • Exemplary supervised clustering algorithms include, but are not limited to, nearest-neighbor analysis, support vector machines, and SPLASH.
  • clinical outcome of each class of patients is either known or determinable.
  • Genes that are differentially expressed in peripheral blood cells (e.g., PBMCs) of one class of patients relative to the other class of patients can be identified.
  • the genes thus identified are substantially correlated with a class distinction between the two classes of patients.
  • the genes thus identified can be used as surrogate markers for predicting clinical outcome of the solid tumor in a patient of interest.
  • patients with a specified solid tumor can be divided into at least two classes based on gene expression profiles in their peripheral blood cells.
  • Methods suitable for this purpose include unsupervised clustering algorithms, such as self-organized maps (SOMs), k-means, principal component analysis, and hierarchical clustering.
  • SOMs self-organized maps
  • k-means principal component analysis
  • hierarchical clustering A substantial number (e.g., at least 50%, 60%, 70%, 80%, 90%, or more) of patients in one class may have a first clinical outcome, and a substantial number of patients in the other class may have a second clinical outcome.
  • Genes that are differentially expressed in the peripheral blood cells of one class of patients relative to the other class of patients can be identified. These genes are prognosis genes for the solid tumor.
  • patients with a specified solid tumor can be divided into three or more classes based on their clinical stratifications or peripheral blood gene expression profiles.
  • Multi-class correlation metrics can be employed to identify genes that are differentially expressed in these classes.
  • Exemplary multi-class correlation metrics include, but are not limited to, GeneCluster 2 software provided by MIT Center for Genome Research at Whitehead Institute (Cambridge, Mass.).
  • nearest-neighbor analysis also known as neighborhood analysis
  • neighborhood analysis is used to analyze gene expression data gathered from nucleic acid arrays.
  • the algorithm for neighborhood analysis is described in Golub, et al., S CIENCE, 286: 531-537 (1999), Slonim, et al., P ROCS. OF THE F OURTH A NNUAL I NTERNATIONAL C ONFERENCE ON C OMPUTATIONAL M OLECULAR B IOLOGY , Tokyo, Japan, April 8-11, p 263-272 (2000), and U.S. Pat. No. 6,647,341, all of which are incorporated herein by reference.
  • Class 0 may include patients having a first clinical outcome
  • class 1 includes patients having a second clinical outcome.
  • Other forms of class distinction can also be employed.
  • a class distinction represents an idealized expression pattern, where the expression level of a gene is uniformly high for samples in one class and uniformly low for samples in the other class.
  • a higher absolute value of a signal-to-noise score indicates that the gene is more highly expressed in one class than in the other.
  • the samples used to derive the signal-to-noise score comprise enriched or purified PBMCs.
  • the signal-to-noise score P(g,c) can represent a correlation between the class distinction and the expression level of gene “g” in PBMCs.
  • the correlation between gene “g” and the class distinction can also be measured by other methods, such as by the Pearson correlation coefficient or the Euclidean distance, as appreciated by those skilled in the art.
  • the significance of the correlation between peripheral blood gene expression patterns and the class distinction can be evaluated using a random permutation test.
  • the correlation between genes and the class distinction can be diagrammatically viewed through a neighborhood analysis plot, in which the y-axis represents the number of genes within various neighborhoods around the class distinction and the x-axis indicates the size of the neighborhood (i.e., P(g,c)). Curves showing different significance levels for the number of genes within corresponding neighborhoods of randomly permuted class distinctions can also be included in the plot.
  • the prognosis genes of the present invention are substantially correlated with a class distinction between two outcome classes.
  • the prognosis genes are above the median significance level in the neighborhood analysis plot. This means that the correlation measure P(g,c) for each prognosis gene is such that the number of genes within the neighborhood of the class distinction having the size of P(g,c) is greater than the number of genes within the corresponding neighborhoods of randomly permuted class distinctions at the median significance level.
  • the employed prognosis genes are above the 10%, 5%, 2%, or 1% significance level.
  • x % significance level means that x % of random neighborhoods contain as many genes as the real neighborhood around the class distinction.
  • Class predictors can be constructed using the prognosis genes of the present invention. These class predictors are useful for assigning class membership to solid tumor patients.
  • the prognosis genes in a class predictor are limited to those shown to be significantly correlated with the class distinction by the permutation test, such as those at above the 1%, 2%, 5%, 10%, 20%, 30%, 40%, or 50% significance level.
  • the expression level of each prognosis gene in a class predictor is substantially higher or substantially lower in PBMCs of one class of patients than in the other class of patients.
  • the prognosis genes in a class predictor have top absolute values of P(g,c).
  • the p-value under a Student's t-test (e.g., two-tailed distribution, two sample unequal variance) for each differentially expressed prognosis gene is no more than 0.05, 0.01, 0.005, 0.001, 0.0005, 0.0001, or less.
  • the class predictors of the present invention have at least 50% accuracy for leave-one-out cross validation. In another embodiment, the class predictors of the present invention have at least 60%, 70%, 80%, 90%, 95%, or 99% accuracy for leave-one-out cross validation.
  • the correlation between peripheral blood gene expression profiles and clinical outcome can be evaluated by statistical methods.
  • Clinical outcome suitable for these analyses includes, but are not limited to, TTP, TTD, and other time-associated clinical indicators.
  • U i is the expression level ranking of a gene of interest
  • V i is the ranking of the clinical outcome
  • n represents the number of patients.
  • the Spearman's rank correlation is similar to the Pearson's correlation except that it is based on ranks and is thus more suitable for data that is not normally distributed. See, for example, Snedecor and Cochran, S TATISTICAL M ETHODS , Eight edition, Iowa State University Press, Ames, Iowa, 503 pp, 1989. The correlation coefficient is tested to assess whether it differs significantly from a value of 0 (i.e., no correlation).
  • the correlation coefficients for each prognosis gene identified by the Spearman's rank correlation can be either positive or negative, provided that the correlation is statistically significant.
  • the p-value for each prognosis gene thus identified is no more than 0.05, 0.01, 0.005, 0.001, 0.0005, 0.0001, or less.
  • the Spearman correlation coefficients of the prognosis genes thus identified have absolute values of at least 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or more.
  • h i (t) is the hazard function that assesses the instantaneous risk of demise at time t, conditional on survival to that time
  • ⁇ (t) is the baseline hazard function
  • x ij is a covariate which may represent, for example, the expression level of prognosis gene j in a peripheral blood sample.
  • Cox proportional hazard model can also be included in Cox proportional hazard model.
  • the terms “demise” or “survival” are not limited to real death or survival. Instead, these terms should be interpreted broadly to cover any type of time-associated events, such as TTP.
  • the p-values for the correlation under Cox proportional hazard regression model are no more than 0.05, 0.01, 0.005, 0.001, 0.0005, 0.0001, or less.
  • the p-values for the prognosis genes identified under Cox proportional hazard regression model can be determined by the likelihood ratio test, Wald test, the Score test, or the log-rank test.
  • the hazard ratios for the prognosis genes thus identified are at least 1.5, 2, 3, 4, 5, or more. In another embodiment, the hazard ratios for the prognosis genes thus identified are no more than 0.67, 0.5., 0.33, 0.25., 0.2, or less.
  • rank tests, scores, measurements, or models can also be employed to identify prognosis genes whose expression profiles in peripheral blood samples are correlated with clinical outcome of solid tumors.
  • These tests, scores, measurements, or models can be either parametric or nonparametric, and the regression may be either linear or non-linear.
  • Many statistical methods and correlation/regression models can be carried out using commercially available programs.
  • telomeres are shortened or telomeres in peripheral blood cells of one class of patients relative to another class of patients. These methods include, but are not limited, RT-PCR, Northern Blot, in situ hybridization, and immunoassays such as ELISA, RIA or Western Blot.
  • the expression levels of genes thus identified can be substantially higher or substantially lower in peripheral blood cells (e.g., PBMCs) of one class of patients than in another class of patients.
  • the average peripheral blood expression level of a prognosis gene in PBMCs of one class of patients can be at least 2, 3, 4, 5, 10, 20, or more folds higher or lower than that in another class of patients.
  • the p-value of an appropriate statistical significance test e.g., Student's t-test
  • for the difference between average expression levels is no more than 0.05, 0.01, 0.005, 0.001, 0.0005, 0.0001, or less.
  • Prognosis genes for other non-blood diseases can be similarly identified according to the present invention, provided that the correlation between peripheral blood gene expression and clinical outcome of these diseases, is statistically significant.
  • the peripheral blood expression patterns of the prognosis genes thus identified are indicative of clinical outcome of these diseases.
  • RCC comprises the majority of all cases of kidney cancer and is one of the ten most common cancers in industrialized countries, comprising 2% of adult malignancies and 2% of cancer-related deaths.
  • prognostic factors and scoring indices have been developed for patients diagnosed with RCC, typified by multivariate assessments of several key indicators.
  • one prognostic scoring system employs the five prognostic factors proposed by Motzer, et al., supra—namely, Karnofsky performance status, serum lactate dehydrognease, hemoglobin, serum calcium, and presence/absence of prior nephrectomy.
  • the present invention identifies numerous RCC prognosis genes whose peripheral blood expression profiles correlate with patient outcome in CCI-779 therapy.
  • the cytostatic mTOR inhibitor CCI-779 was evaluated in RCC patients for its anti-cancer effect.
  • PBMCs collected prior to CCI-779 therapy were analyzed on oligonucleotide arrays in order to determine whether mononuclear cells from RCC patients possessed transcriptional patterns predictive of patient outcome.
  • the results of both supervised and unsupervised analyses indicated that transcriptional profiles in the surrogate tissue of PBMCs from RCC patients prior to treatment with CCI-779 are significantly correlated with patient outcome.
  • PBMCs peripheral blood of 45 advanced RCC patients (18 females and 27 males) participating in a phase 2 clinical trial study.
  • Written informed consent for the pharmacogenomic portion of the clinical study was received for all individuals and the project was approved by the local Institutional Review Boards at the participating clinical sites.
  • RCC tumors of patients were classified at the clinical sites as conventional (clear cell) carcinomas (24), granular (1), papillary (3), or mixed subtypes (7).
  • Ten tumors were classified as unknown.
  • RCC patients were primarily of Caucasian descent (44 Caucasian, 1 African-American) and had a mean age of 58 years (range of 40-78 years).
  • Inclusion criteria included patients with histologically confirmed advanced renal cancer who had received prior therapy for advanced disease, or who had not received prior therapy for advanced disease but were not appropriate candidates to receive high doses of IL-2 therapy.
  • Other inclusion criteria included patients with (1) bi-dimensionally measurable evidence of disease; (2) evidence of progression of the disease prior to study entry; (3) an age of 18 years or older; (4) ANC>1500/ ⁇ L, platelet>100,000/ ⁇ L and hemoglobin>8.5 g/dL; (5) adequate renal function evidenced by serum creatinine ⁇ 1.5 ⁇ upper limit of normal; (6) adequate hepatic function evidenced by biliruubin ⁇ 1.5 ⁇ upper limit of normal and AST ⁇ 3 ⁇ upper limit of normal (or AST ⁇ 5 ⁇ upper limit of normal if liver metastases were present); (7) serum cholesterol ⁇ 350 mg/dL, triglycerides ⁇ 300 mg/dL; (8) ECOG performance status 0-1; and (9) a life expectancy of at least 12 weeks.
  • Exclusion criteria included patients who had (1) the presence of known CNS metastases; (2) surgery or radiotherapy within 3 weeks of start of dosing; (3) chemotherapy or biologic therapy for RCC within 4 weeks of start of dosing; (4) treatment with a prior investigational agent within 4 weeks of start of dosing; (5) immunocompromised status including those known to be HIV positive, or receiving concurrent use of immunosuppressive agents including corticosteroids; (6) active infections; (7) required treatment with anticonvulsant therapy; (8) presence of unstable angina/myocardial infarction within 6 months/ongoing treatment of life-threatening arrythmia; (9) history of prior malignancy in past 3 years; (10) hypersensitivity to macrolide antibiotics; and (11) pregnancy or any other illness which would substantially increase the risk associated with participation in the study.
  • CCI-779 is an ester analog of the immunosuppressant rapamycin and as such is a potent, selective inhibitor of the mammalian target of rapamycin.
  • the mammalian target of rapamycin (mTOR) activates multiple signaling pathways, including phosphorylation of p70s6kinase, which results in increased translation of 5′ TOP mRNAs encoding proteins involved in translation and entry into the G1 phase of the cell cycle.
  • mTOR mammalian target of rapamycin
  • CCI-779 functions as a cytostatic and immunosuppressive agent.
  • Tumor size was measured in centimeters and reported as the product of the longest diameter and its perpendicular.
  • Measurable disease was defined as any bidimensionally measurable lesion where both diameters>1.0 cm by CT-scan, X-ray or palpation.
  • Tumor response was determined by the sum of the products of all measurable lesions.
  • the categories for assignment of clinical response were given by the clinical protocol definitions (i.e., progressive disease, stable disease, minor response, partial response, and complete response). The category for assignment of prognosis under the Motzer risk assessment (favorable vs intermediate vs poor) was also used.
  • HgU95A genechips (manufactured by Affymetrix) were used to detect baseline expression profiles in PBMCs of the RCC patients prior to the CCI-779 therapy.
  • Each HgU95A genechip comprises over 12,600 human sequences according to the Affymetrix Expression Analysis Technical Manual.
  • RNA transcripts were first isolated from PBMCs of the RCC patients.
  • cRNA was then prepared and hybridized to the genechips according to protocols described in the Affymetrix's Expression Analysis Technical Manual. Hybridization signals were collected, scaled, and normalized before being subject to further analysis. In one example, the log of the expression level for each gene was normalized across the samples such that the mean is zero and the standard deviation is one.
  • the expression profiling analysis revealed that of the 12,626 genes on the HgU95A chip, 5,424 genes met the initial criteria (i.e., at least 1 present call across the data set and at least 1 frequency ⁇ 10 ppm). On average, 4,023 transcripts were detected as “present” in any given RCC PBMC profile.
  • pairwise correlations were calculated to assess the association between gene expression levels measured by HgU95A Affymetrix microarrays and continuous measures of clinical outcome. Correlations were run using expression levels from each of 5,424 qualifiers that passed the initial criteria. Correlations were run for two clinical measures (TTD and TTP) and for one measure of baseline expression level (log 2 -transformed scaled frequency in units of ppm).
  • Spearman's rank correlations were computed. The p-value for the hypothesis that the correlation was equal to 0 was calculated for each pairwise correlation. For each comparison between clinical outcome and gene expression, the number of tests that were nominally significant out of the 5,424 tests performed was calculated for five Type I (i.e. false-positive) error levels. To adjust for the fact that 5,424 non-independent tests were performed, a permutation-based approach was employed to evaluate how often the observed number of significance tests would be found under the null hypothesis of no correlation.
  • Tables 2a and 2b The overall results for Spearman's rank correlation comparisons of clinical outcome with baseline expression levels (log 2 -transformed scaled frequency) are summarized in Tables 2a and 2b. Each table shows alpha confidence levels (“ ⁇ ”), the observed numbers of transcripts that have nominally significant Spearman correlations with the clinical outcome of interest (“Observed Number”), and the percentage of permutations for which number of nominally significant Spearman correlations equals or exceeds the number observed (“%-age of Permutations”). Evidence for association between clinical outcome and baseline gene expression in PBMCs was significant for both TTD and TTP.
  • Table 3 lists the results of the Spearman's rank correlation analyses for all of the 5,424 genes that met the initial criteria.
  • Each gene has a corresponding qualifier on the HgU95A genechip, and each qualifier represents multiple oligonucleotide probes that are stably attached to discrete regions on the HgU95A genechip.
  • RNA transcripts of a gene, or the complements thereof are expected to hybridize under nucleic acid array hybridization conditions to the corresponding qualifier on the HgU95A genechip.
  • a polynucleotide can hybridize to a qualifier if the polynucleotide, or the complement thereof, can hybridize to at least one oligonucleotide probe of the qualifier.
  • the polynucleotide or the complement thereof can hybridize to at least 50%, 60%, 70%, 80%, 90% or 100% of all of the oligonucleotide probes of the qualifier.
  • Each gene or qualifier in Table 3 may have a corresponding SEQ ID NO or Entrez accession number from which the oligonucleotide probes of the qualifier can be derived.
  • a polypeptide capable of hybridizing to a qualifier can also hybridize to the sequence of the corresponding SEQ ID NO or Entrez accession number, or the complement thereof.
  • the sequence of each Entrez accession number can be obtained from the Entrez nucleotide database at the National Center of Biotechnology Information (NCBI).
  • NCBI National Center of Biotechnology Information
  • the Entrez nucleotide database collects sequences from several sources, including GenBank, RefSeq, and PDB. Each SEQ ID NO may be derived from the sequence of the corresponding Entrez accession number.
  • Table 4 shows the Entrez and Unigene accession numbers for all of the qualifiers on the HgU95A genechip that met the initial criteria.
  • any ambiguous residue (“n”) in a SEQ ID NO can be determined by a variety of methods.
  • the ambiguous residues in a SEQ ID NO are determined by aligning the SEQ ID NO to a corresponding genomic sequence obtained from a human genome sequence database.
  • the ambiguous residues in a SEQ ID NO are determined based on the sequence of the corresponding Entrez accession number.
  • the ambiguous residues are determined by re-sequencing the SEQ ID NO.
  • Genes associated with each qualifier on the HgU95A genechip can be identified based on the annotations provided by Affymetrix. All of the genes thus identified are listed in Tables 3 and 5. These genes can also be identified based on their corresponding Entrez or Unigene accession numbers. In addition, these genes can be determined by BLAST searching their corresponding SEQ ID NOs, or the unambiguous segments thereof, against a human genome sequence database. Suitable human genome sequence databases for this purpose include, but are not limited to, the NCBI human genome database. The NCBI provides BLAST programs, such as “blastn,” for searching its sequence databases.
  • the BLAST search of the NCBI human genome database is carried out by using an unambiguous segment (e.g., the longest unambiguous segment) of a SEQ ID NO.
  • Gene(s) that aligns to the unambiguous segment with significant sequence identity can be identified.
  • the identified gene(s) has at least 95%, 96%, 97%, 98%, 99%, or more sequence identity with the unambiguous segment.
  • Table 6a lists examples of genes whose expression levels are positively correlated with TTP.
  • Table 6b depicts examples of genes whose expression levels are negatively correlated with TTP.
  • Table 6c provides examples of genes whose expression levels are positively correlated with TTD.
  • Table 6d shows examples of genes whose expression levels are negatively correlated with TTD. Correlation coefficients, p-values, and the corresponding qualifiers are also indicated for each gene in Tables 6a, 6b, 6c, and 6d.
  • the present invention contemplates the use of any other gene that can hybridize under stringent or nucleic acid array hybridization conditions to a qualifier identified in the present invention.
  • genes may include hypothetical or putative genes that are supported by EST or mRNA data. The expression profiles of these genes may correlate with patient clinical outcome.
  • a gene can hybridize to a qualifier if an RNA transcript of the gene can hybridize to at least one oligonucleotide probe of the qualifier. In many cases, an RNA transcript of the gene can hybridize to at least 50%, 60%, 70%, 80%, 90%, or more oligonucleotide probes of the qualifier.
  • Cox proportional hazard regression model was employed to assess the correlation between baseline PBMC gene expression levels and clinical outcome.
  • Cox model can take into account the effects of censoring on correlations of gene expression with TTD (or Survival as of last known date alive) and TTP (or progression-free status as of last known date alive).
  • TTD or Survival as of last known date alive
  • TTP or progression-free status as of last known date alive
  • 4 had censored data for TTP
  • 15 had censored data for TTD.
  • Cox regression can identify genes significantly correlated with survival and disease progression for any given ⁇ -confidence level.
  • a similar permutation strategy can be used to affirm any correlation between baseline expression profiles and clinical outcome.
  • models were fit using expression levels from each of the 5,424 qualifiers that passed the initial filtering criteria in the 45 baseline samples.
  • TTP and TTD were tested for their association with log2-transformed scaled frequency at baseline.
  • a SAS program was used to generate the estimates in Tables 7a and 7b. Tables 7a and 7b demonstrate a strong correlation between TTP/TTD and baseline gene expression.
  • Table 8 lists the results of Cox proportional hazard modeling for all of the 5,424 genes that met the initial criteria. Hazard ratios and p-values (for the hypothesis that the risk coefficient was equal to 1, i.e., no risk) are indicated for each gene. Examples of genes that are indicative of high risk for TTP or TTD are shown in Tables 9a or 9c, respectively. These genes have hazard ratios of at least 3. Examples of genes that are indicative of low risk for TTP or TTD are described in Tables 9b or 9d, respectively. These genes have hazard ratios of no more than 0.333.
  • nearest-neighbor analysis was employed to identify multivariate expression patterns in PBMCs of patients that were correlated with clinical responses. This approach included nearest-neighbor-based identification of transcripts most correlated with the class distinction of interest, random permutation of the sample labels to determine the significance of the discovered gene classifiers, and evaluation of the accuracy of various predictive models containing different numbers of genes by leave-one-out cross validation.
  • nearest-neighbor analysis and supervised class prediction were performed using Genecluster version 2.0 which has been described by Golub, et al., supra, and is available at www.genome.wi.mit.edu/cancer/software/genecluster2.html.
  • Genecluster version 2.0 which has been described by Golub, et al., supra, and is available at www.genome.wi.mit.edu/cancer/software/genecluster2.html.
  • All raw expression data were log transformed and normalized to have a mean value of zero and a variance of one.
  • Class prediction was carried out using a k-nearest-neighbors algorithm as described in Armstrong, et al., N ATURE G ENETICS, 30:41-47 (2002), which is incorporated herein by reference.
  • This algorithm assigns a test sample to a class by identifying the k-nearest samples in the training set and then choosing the most common class among these k-nearest-neighbors. See Armstrong, et al., supra.
  • distances can be defined by a Euclidean metric on the basis of the expression levels of a specified number of genes.
  • FIGS. 1A-1D illustrate the comparison of short and long term survivors.
  • the class distinction is between RCC patients who had TTD of less than 150 days (the “shorter” class) and RCC patients who had TTD of greater than 550 days (the “longer” class).
  • the relative expression levels of the class-correlated gene (rows in FIG. 1A ) were indicated for each patient (columns in FIG. 1A ) according to the normalized expression level scale.
  • FIG. 1B depicts the comparison of the signal to noise similarity metric scores (S2N, i.e.,
  • S2N signal to noise similarity metric scores
  • Table 10 also shows the HgU95A qualifier for each gene (“Qualifier”), the rank of each gene (“Rank #”), the class within which the gene is more highly expressed (“Class”), the S2N score (“Score”), the S2N score under a random permutation analysis at the 1% significance level (“Perm 1%”), the S2N score under a random permutation analysis at the 5% significance level (“Perm 5%”), and the S2N score under a random permutation analysis at the median significance level (“Perm (user)”).
  • the genes are ranked based on their respective S2N scores.
  • FIG. 1D demonstrates the cross validation results for each sample using the 58-gene predictor.
  • PS prediction strengths
  • FIGS. 2A-2E A variety of other clinically relevant stratifications were also performed and relative expression levels of the optimally-sized gene classifiers in each analysis are summarized in FIGS. 2A-2E .
  • the relative expression levels of the genes (rows) in each classifier are indicated for each patient (columns) according to the scale of FIG. 1A .
  • FIG. 2A shows the relative gene expression levels of a 42-gene classifier for the comparison of patients with intermediate versus poor Motzer risk classification. Genes in this classifier are described in Table 11. The baseline expression levels of these genes in PBMCs of RCC patients are predictive of a patient's classification under Motzer risk assessment.
  • FIG. 2B shows the relative gene expression levels for an 18-gene classifier identified in the comparison of patients with progressive disease versus any other clinical response.
  • FIG. 2C demonstrates the relative gene expression levels for a 6-gene classifier identified in the comparison of patients in the lower versus upper quartiles of time to disease progression. Genes in this classifier are illustrated in Table 12.
  • FIG. 2D shows the relative gene expression levels for a 52-gene classifier identified in the comparison of patients in the lower versus upper quartiles of survival/time to death.
  • FIG. 2E depicts the relative expression levels for a 12-gene classifier identified in the comparison of patients with early (time to disease progression ⁇ 106 days) versus all other times to disease progression (TTP ⁇ 106 days). Genes in this classifier are described in Table 13.
  • “Sensitivity” as used herein refers to the ratio of correct positive calls over the total of true positive calls plus false negative calls. “Specificity” refers to the ratio of correct negative calls over the total of true negative calls plus false positive calls.
  • the genes identified in FIGS. 1 A and 2 A- 2 E and Tables 10-13, or the classifiers derived therefrom, can be used to assign an RCC patient to a respective clinical class selected from Table 14.
  • unsupervised clustering was employed to identify genes that are correlated with survival.
  • One of the primary endpoints of a clinical trial or a therapeutic treatment is survival.
  • the above-described gene classifiers do not predict short term survival with supreme sensitivity and specificity (such as over 90%, 95%, or more). This might be due to heterogeneity in PBMC expression patterns from patients binned arbitrarily into different survival categories that precludes highly accurate prediction using forced-type supervised approaches.
  • a pharmacogenomic assay capable of identifying short-term and long-term survivors in a significant fraction of the intended treatment population would still have obvious benefit, in terms of clinical prognosis.
  • an unsupervised hierarchical clustering approach using all genes passing the initial criteria (5,424 genes total) was employed.
  • the unsupervised hierarchical clustering was performed according to the procedure described in Eisen, et al., P ROC N ATL A CAD S CI U.S.A., 95:14863-14868 (1998).
  • data were log transformed and normalized to have a mean value of zero and a variance of one.
  • Hierarchical clustering results were generated using average linkage clustering and an uncentered correlation similarity metric.
  • the majority of patients in cluster A possessed significantly shorter survival than the majority of patients in cluster C, suggesting that expression differences in these two subclusters of patients could be predictive of survival in the majority of patients in these subpopulations.
  • RCC patient PBMC expression profiles in the poor prognosis cluster (“A”) are indicated by the box around subcluster “A” in which 9 out of 12 patients exhibited survival of less than 365 days.
  • RCC patient PBMC expression profiles in the good prognosis cluster (“C”) are indicated by the box around subcluster “C” in which 10 out of 12 patients exhibited survival of 365 or more days.
  • prognostic Motzer scores were distinct between subclusters A and C, as indicated in FIG. 3A .
  • FIG. 3B shows the baseline expression patterns of a group of selected genes in subclusters A-D. Elevated or decreased expression values relative to the average expression value across all experiments are indicated according to the scale of FIG. 1A .
  • a nearest-neighbor algorithm was employed to identify the transcripts in the subsets of PBMCs that are significantly correlated with good and poor prognosis signatures.
  • the relative expression levels of an optimally-sized gene classifier derived from this analysis are shown in FIG. 5A .
  • the gene classifier was composed of 158 genes. Because the good prognosis and poor prognosis clusters were identified based upon their differences in gene expression, random permutation of this nearest-neighbor analyses showed the genes in the classifier to be significantly correlated as expected (p ⁇ 0.01).
  • the performance of the 158-gene classifier demonstrated 79% overall accuracy, correctly identifying 9 of 11 patients with short survival times (less than 1 year, 82% sensitivity) and 10 of 13 patients with long term survival times (greater than 1 year, 77% specificity). See FIG. 5B .
  • the confidence scores were calculated for each sample in the analysis. For the purposes of illustration, prediction strengths accompanying calls of “survival ⁇ 1 year” were assigned positive values, and prediction strengths accompanying calls of “survival ⁇ 1 year” were assigned negative values. Asterisks identify the false positives in this clinical assay designed to identify short survival times, and arrowheads indicate false negatives.
  • prognosis genes for other solid tumors can be similarly identified according to the present invention. These genes are differentially expressed in peripheral blood cells of solid tumor patients having different clinical outcomes.
  • the prognosis genes of the present invention can be used as surrogate markers for the prognosis of solid tumors.
  • the prognosis genes of the present invention can also be used to select optimal treatments of solid tumors. For instance, clinical outcomes of different treatments for a solid tumor can be analyzed by using peripheral blood expression profiling. Treatments with favorable prognoses are selected for patients of interest.
  • any solid tumor, treatment, or clinical outcome can be assessed by the present invention.
  • clinical outcome can be measured by TTP (e.g., less than or greater than a specified period), TTD (e.g., less than or greater than a specified period), progressive disease, non-progressive disease, stable disease, complete response, partial response, minor response, or a combination thereof.
  • Clinical outcome can also be prognosticated based on clinical classifications under traditional risk assessment methods (such as Motzer risk assessment for RCC, as described in Motzer, et al., supra).
  • non-responsiveness to a therapeutic treatment is also considered a measurable outcome.
  • the peripheral blood expression profile of one or more prognosis genes in the patient of interest is compared to at least one reference expression profile. Any number of prognosis genes can be used.
  • the PBMC expression profiles of the prognosis genes are correlated with patient outcome under a class-based correlation metric (such as nearest-neighbor analysis) or a statistical method (such as Spearman's rank correlation or Cox proportional hazard regression model).
  • the prognosis genes are differentially expressed in PBMCs of one class of patients as compared to another class of patients. Both classes of patients have a solid tumor, and each class of patients has a different clinical outcome.
  • the PBMC expression level of each prognosis gene is substantially higher or substantially lower in PBMCs of one class of patients than that in another class of patients.
  • the prognosis genes are substantially correlated with a class distinction between two classes of patients, where the two classes of patients have the same disease as the patient of interest, and each class of patients has a different clinical outcome. In many cases, the prognosis genes are correlated with the class distinction at above the 50%, 25%, 10%, 5%, or 1% significance level under random permutation tests.
  • the reference expression profile(s) can be determined concurrently with the expression profile of the patient of interest.
  • the reference expression profile(s) can also be predetermined or prerecorded in an electronic or another storage medium.
  • the reference expression profile(s) is an average expression profile of the prognosis genes in peripheral blood samples of reference patients. Any averaging algorithm can be used to prepare the reference expression profile(s).
  • the reference patients have the same solid tumor as the patient of interest, and the clinical outcome of the reference patients is either known or determinable.
  • the reference patients can be divided into at least two classes, each class having a different respective clinical outcome.
  • the peripheral blood expression profile of the prognosis genes in each class of the reference patients constitutes a separate reference profile.
  • the expression profile of the patient of interest and the reference expression profile(s) can be in any form.
  • the expression profiles comprise the expression level of each prognosis gene used in the comparison.
  • the expression levels can have absolute, normalized, or relative values. Suitable normalization procedures include, but are not limited to, those used in nucleic acid array gene expression analyses or those described in Hill, et al., G ENOME B IOL, 2:research0055.1-0055.13 (2001).
  • the expression levels are normalized such that the mean is zero and the standard deviation is one.
  • the expression levels are normalized based on internal or external controls, as appreciated by those skilled in the art.
  • the expression levels are normalized against one or more control transcripts with known abundances in blood samples.
  • the expression profile of the patient of interest and the reference expression profile(s) are constructed using the same or comparable methodology.
  • the expression profiles comprise one or more ratios between the expression levels of different prognosis genes.
  • the expression profiles can also include other measures that are capable of representing gene expression patterns.
  • the peripheral blood samples used in the present invention can be either whole blood samples, or samples comprising enriched PBMCs.
  • the peripheral blood samples from the reference patients comprise enriched or purified PBMCs
  • the peripheral blood sample from the patient of interest is a whole blood sample.
  • all of the peripheral blood samples employed in the analysis comprise enriched or purified PBMCs.
  • the peripheral blood samples are prepared from the patient of interest and the reference patients by using the same or comparable procedures.
  • blood samples can also be employed in the present invention, provided that a statistically significant correlation exists between patient outcome and the gene expression profile in these blood samples.
  • peripheral blood samples used in the present invention can be isolated from respective patients at any disease or treatment stage, provided that the correlation between the gene expression patterns in these peripheral blood samples and clinical outcome is statistically significant.
  • clinical outcome is measured by patients' response to a therapeutic treatment, and all of the blood samples used in the analysis are isolated prior to the therapeutic treatment.
  • the expression profiles derived from these blood samples are baseline expression profiles for the therapeutic treatment.
  • the expression level of a gene can be determined by measuring the level of the RNA transcript(s) of the gene. Suitable methods include, but are not limited to, quantitative RT-PCR, Northern blot, in situ hybridization, slot-blotting, nuclease protection assay, and nucleic acid array (including bead array).
  • the expression level of a gene can also be determined by measuring the level of the polypeptide(s) encoded by the gene. Suitable methods include, but are not limited to, immunoassays (such as ELISA, RIA, FACS, or Western blot), 2-dimensional gel electrophoresis, mass spectrometry, or protein arrays.
  • the expression level of a prognosis gene is determined by measuring the RNA transcript level of the gene in a peripheral blood sample.
  • RNA can be isolated from the peripheral blood sample using a variety of methods. Exemplary methods include guanidine isothiocyanate/acidic phenol method, the TRIZOL® Reagent (Invitrogen), or the Micro-FastTrackTM 2.0 or FastTrackTM 2.0 mRNA Isolation Kits (Invitrogen).
  • the isolated RNA can be either total RNA or mRNA.
  • the isolated RNA can be amplified to cDNA or cRNA before subsequent detection or quantitation. The amplification can be either specific or non-specific. Suitable amplification methods include, but are not limited to, reverse transcriptase PCR (RT-PCR), isothermal amplification, ligase chain reaction, and Qbeta replicase.
  • the amplification protocol employs reverse transcriptase.
  • the isolated mRNA can be reverse transcribed into cDNA using a reverse transcriptase, and a primer consisting of oligo d(T) and a sequence encoding the phage T7 promoter.
  • the cDNA thus produced is single-stranded.
  • the second strand of the cDNA is synthesized using a DNA polymerase, combined with an RNase to break up the DNA/RNA hybrid.
  • T7 RNA polymerase is added, and cRNA is then transcribed from the second strand of the doubled-stranded cDNA.
  • the amplified cDNA or cRNA can be detected or quantitated by hybridization to labeled probes.
  • the cDNA or cRNA can also be labeled during the amplification process and then detected or quantitated.
  • quantitative RT-PCR (such as TaqMan, ABI) is used for detecting or comparing the RNA transcript level of a prognosis gene of interest.
  • Quantitative RT-PCR involves reverse transcription (RT) of RNA to cDNA followed by relative quantitative PCR (RT-PCR).
  • PCR the number of molecules of the amplified target DNA increases by a factor approaching two with every cycle of the reaction until some reagent becomes limiting. Thereafter, the rate of amplification becomes increasingly diminished until there is not an increase in the amplified target between cycles.
  • a graph is plotted on which the cycle number is on the X axis and the log of the concentration of the amplified target DNA is on the Y axis, a curved line of characteristic shape can be formed by connecting the plotted points. Beginning with the first cycle, the slope of the line is positive and constant. This is said to be the linear portion of the curve. After some reagent becomes limiting, the slope of the line begins to decrease and eventually becomes zero. At this point the concentration of the amplified target DNA becomes asymptotic to some fixed value. This is said to be the plateau portion of the curve.
  • the concentration of the target DNA in the linear portion of the PCR is proportional to the starting concentration of the target before the PCR is begun.
  • concentration of the PCR products of the target DNA in PCR reactions that have completed the same number of cycles and are in their linear ranges, it is possible to determine the relative concentrations of the specific target sequence in the original DNA mixture. If the DNA mixtures are cDNAs synthesized from RNAs isolated from different tissues or cells, the relative abundances of the specific mRNA from which the target sequence was derived may be determined for the respective tissues or cells. This direct proportionality between the concentration of the PCR products and the relative mRNA abundances is true in the linear range portion of the PCR reaction.
  • the final concentration of the target DNA in the plateau portion of the curve is determined by the availability of reagents in the reaction mix and is independent of the original concentration of target DNA. Therefore, in one embodiment, the sampling and quantifying of the amplified PCR products are carried out when the PCR reactions are in the linear portion of their curves.
  • relative concentrations of the amplifiable cDNAs can be normalized to some independent standard, which may be based on either internally existing RNA species or externally introduced RNA species. The abundance of a particular mRNA species may also be determined relative to the average abundance of all mRNA species in the sample.
  • the PCR amplification utilizes internal PCR standards that are approximately as abundant as the target. This strategy is effective if the products of the PCR amplifications are sampled during their linear phases. If the products are sampled when the reactions are approaching the plateau phase, then the less abundant product may become relatively over-represented. Comparisons of relative abundances made for many different RNA samples, such as is the case when examining RNA samples for differential expression, may become distorted in such a way as to make differences in relative abundances of RNAs appear less than they actually are. This can be improved if the internal standard is much more abundant than the target. If the internal standard is more abundant than the target, then direct linear comparisons may be made between RNA samples.
  • RT-PCR is performed as a relative quantitative RT-PCR with an internal standard in which the internal standard is an amplifiable cDNA fragment that is larger than the target cDNA fragment and in which the abundance of the mRNA encoding the internal standard is roughly 5-100 fold higher than the mRNA encoding the target.
  • This assay measures relative abundance, not absolute abundance of the respective mRNA species.
  • the relative quantitative RT-PCR uses an external standard protocol. Under this protocol, the PCR products are sampled in the linear portion of their amplification curves. The number of PCR cycles that are optimal for sampling can be empirically determined for each target cDNA fragment.
  • the reverse transcriptase products of each RNA population isolated from the various samples can be normalized for equal concentrations of amplifiable cDNAs. While empirical determination of the linear range of the amplification curve and normalization of cDNA preparations are tedious and time-consuming processes, the resulting RT-PCR assays may, in certain cases, be superior to those derived from a relative quantitative RT-PCR with an internal standard.
  • nucleic acid arrays are used for detecting or comparing the expression profiles of a prognosis gene of interest.
  • the nucleic acid arrays can be commercial oligonucleotide or cDNA arrays. They can also be custom arrays comprising concentrated probes for the prognosis genes of the present invention. In many examples, at least 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, or more of the total probes on a custom array of the present invention are probes for solid tumor prognosis genes. These probes can hybridize under stringent or nucleic acid array hybridization conditions to the RNA transcripts, or the complements thereof, of the corresponding prognosis genes.
  • stringent conditions are at least as stringent as, for example, conditions G-L shown in Table 17.
  • “Highly stringent conditions” are at least as stringent as conditions A-F shown in Table 17.
  • hybridization is carried out under the hybridization conditions (Hybridization Temperature and Buffer) for about four hours, followed by two 20-minute washes under the corresponding wash conditions (Wash Temp. and Buffer). TABLE 17 Stringency Conditions Stringency Polynucleotide Hybrid Hybridization Wash Temp.
  • the hybrid length is assumed to be that of the hybridizing polynucleotide.
  • the hybrid length can be determined by aligning the sequences of the polynucleotides and identifying the region or regions of optimal sequence complementarity.
  • H SSPE (1x SSPE is 0.15M NaCl, 10 mM NaH 2 PO 4 , and 1.25 mM EDTA, pH 7.4) can be substituted for SSC (1x SSC is 0.15M NaCl and 15 mM sodium citrate) in the hybridization and wash buffers.
  • a nucleic acid array of the present invention includes at least 2, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, 250, or more different probes.
  • Each of these probes is capable of hybridizing under stringent or nucleic acid array hybridization conditions to a different respective prognosis gene of the present invention.
  • Multiple probes for the same prognosis gene can be used on the same nucleic acid array.
  • the probe density on the array can be in any range. For instance, the density can be at least (or no more than) 5, 10, 25, 50, 100, 200, 300, 400, or 500, 1,000, 2,000, 3,000, 4,000, 5,000, or more probes/cm 2 .
  • the probes can be DNA, RNA, PNA, or a modified form thereof.
  • the nucleotide residues in each probe can be either naturally occurring residues (such as deoxyadenylate, deoxycytidylate, deoxyguanylate, deoxythymidylate, adenylate, cytidylate, guanylate, and uridylate), or synthetically produced analogs that are capable of forming desired base-pair relationships.
  • these analogs include, but are not limited to, aza and deaza pyrimidine analogs, aza and deaza purine analogs, and other heterocyclic base analogs, wherein one or more of the carbon and nitrogen atoms of the purine and pyrimidine rings are substituted by heteroatoms, such as oxygen, sulfur, selenium, and phosphorus.
  • the polynucleotide backbones of the probes can be either naturally occurring (such as through 5′ to 3′ linkage), or modified.
  • the nucleotide units can be connected via non-typical linkage, such as 5′ to 2′ linkage, so long as the linkage does not interfere with hybridization.
  • peptide nucleic acids in which the constitute bases are joined by peptide bonds rather than phosphodiester linkages, can be used.
  • the probes for the prognosis genes can be stably attached to discrete regions on the nucleic acid array.
  • stably attached it means that a probe maintains its position relative to the attached discrete region during hybridization and signal detection.
  • the position of each discrete region on the nucleic acid array can be either known or determinable. All of the methods known in the art can be used to make the nucleic acid arrays of the present invention.
  • nuclease protection assays are used to quantitate RNA transcript levels in peripheral blood samples.
  • nuclease protection assays There are many different versions of nuclease protection assays. The common characteristic of these nuclease protection assays is that they involve hybridization of an antisense nucleic acid with the RNA to be quantified. The resulting hybrid double-stranded molecule is then digested with a nuclease that digests single-stranded nucleic acids more efficiently than double-stranded molecules. The amount of antisense nucleic acid that survives digestion is a measure of the amount of the target RNA species to be quantified. Examples of suitable nuclease protection assays include the RNase protection assay provided by Ambion, Inc. (Austin, Tex.).
  • Hybridization probes or amplification primers for the prognosis genes of the present invention can be prepared by using any method known in the art.
  • the probes/primers for these genes can be derived from the corresponding SEQ ID NOs, Entrez accession numbers, or EST or mRNA sequences.
  • the probes/primers for each prognosis gene significantly diverge from the sequences of other prognosis genes. This can be achieved by checking potential probe/primer sequences against a human genome sequence database, such as the Entrez database at the NCBI.
  • a human genome sequence database such as the Entrez database at the NCBI.
  • One algorithm suitable for this purpose is the BLAST algorithm. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold.
  • the initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence to increase the cumulative alignment score.
  • Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always>0) and N (penalty score for mismatching residues; always ⁇ 0).
  • the BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. These parameters can be adjusted for different purposes, as appreciated by those skilled in the art.
  • the expression levels of the prognosis genes of the present invention are determined by measuring the levels of polypeptides encoded by the prognosis genes.
  • Methods suitable for this purpose include, but are not limited to, immunoassays such as ELISA, RIA, FACS, dot blot, Western Blot, immunohistochemistry, and antibody-based radioimaging.
  • high-throughput protein sequencing, 2-dimensional SDS-polyacrylamide gel electrophoresis, mass spectrometry, or protein arrays can be used.
  • ELISAs are used for detecting the levels of the target proteins.
  • antibodies capable of binding to the target proteins are immobilized onto selected surfaces exhibiting protein affinity, such as wells in a polystyrene or polyvinylchloride microtiter plate. Samples to be tested are then added to the wells. After binding and washing to remove non-specifically bound immunocomplexes, the bound antigen(s) can be detected. Detection can be achieved by the addition of a second antibody which is specific for the target proteins and is linked to a detectable label.
  • Detection can also be achieved by the addition of a second antibody, followed by the addition of a third antibody that has binding affinity for the second antibody, with the third antibody being linked to a detectable label.
  • a second antibody followed by the addition of a third antibody that has binding affinity for the second antibody, with the third antibody being linked to a detectable label.
  • the samples suspected of containing the target proteins are immobilized onto the well surface and then contacted with the antibodies. After binding and washing to remove non-specifically bound immunocomplexes, the bound antigen is detected. Where the initial antibodies are linked to a detectable label, the immunocomplexes can be detected directly. The immunocomplexes can also be detected using a second antibody that has binding affinity for the first antibody, with the second antibody being linked to a detectable label.
  • Another exemplary ELISA involves the use of antibody competition in the detection.
  • the target proteins are immobilized on the well surface.
  • the labeled antibodies are added to the well, allowed to bind to the target proteins, and detected by means of their labels.
  • the amount of the target proteins in an unknown sample is then determined by mixing the sample with the labeled antibodies before or during incubation with coated wells. The presence of the target proteins in the unknown sample acts to reduce the amount of antibody available for binding to the well and thus reduces the ultimate signal.
  • Different ELISA formats can have certain features in common, such as coating, incubating or binding, washing to remove non-specifically bound species, and detecting the bound immunocomplexes. For instance, in coating a plate with either antigen or antibody, the wells of the plate can be incubated with a solution of the antigen or antibody, either overnight or for a specified period of hours. The wells of the plate are then washed to remove incompletely adsorbed material. Any remaining available surfaces of the wells are then “coated” with a nonspecific protein that is antigenically neutral with regard to the test samples. Examples of these nonspecific proteins include bovine serum albumin (BSA), casein and solutions of milk powder.
  • BSA bovine serum albumin
  • the coating allows for blocking of nonspecific adsorption sites on the immobilizing surface and thus reduces the background caused by nonspecific binding of antisera onto the surface.
  • a secondary or tertiary detection means can be used. After binding of a protein or antibody to the well, coating with a non-reactive material to reduce background, and washing to remove unbound material, the immobilizing surface is contacted with the control or clinical or biological sample to be tested under conditions effective to allow immunocomplex (antigen/antibody) formation. These conditions may include, for example, diluting the antigens and antibodies with solutions such as BSA, bovine gamma globulin (BGG) and phosphate buffered saline (PBS)/Tween and incubating the antibodies and antigens at room temperature for about 1 to 4 hours or at 4° C. overnight. Detection of the immunocomplex is facilitated by using a labeled secondary binding ligand or antibody, or a secondary binding ligand or antibody in conjunction with a labeled tertiary antibody or third binding ligand.
  • BSA bovine gamma globulin
  • PBS phosphate buffered saline
  • the contacted surface can be washed so as to remove non-complexed material.
  • the surface may be washed with a solution such as PBS/Tween, or borate buffer.
  • a solution such as PBS/Tween, or borate buffer.
  • the second or third antibody can have an associated label to allow detection.
  • the label is an enzyme that generates color development upon incubating with an appropriate chromogenic substrate.
  • a urease e.g., glucose oxidase, alkaline phosphatase or hydrogen peroxidase-conjugated antibody for a period of time and under conditions that favor the development of further immunocomplex formation (e.g., incubation for 2 hours at room temperature in a PBS-containing solution such as PBS-Tween).
  • the amount of label can be quantified, e.g., by incubation with a chromogenic substrate such as urea and bromocresol purple or 2,2′-azido-di-(3-ethyl)-benzthiazoline-6-sulfonic acid (ABTS) and H 2 O 2 , in the case of peroxidase as the enzyme label. Quantitation can be achieved by measuring the degree of color generation, e.g., using a spectrophotometer.
  • a chromogenic substrate such as urea and bromocresol purple or 2,2′-azido-di-(3-ethyl)-benzthiazoline-6-sulfonic acid (ABTS) and H 2 O 2 , in the case of peroxidase as the enzyme label.
  • Quantitation can be achieved by measuring the degree of color generation, e.g., using a spectrophotometer.
  • RIA radioimmunoassay
  • An exemplary RIA is based on the competition between radiolabeled-polypeptides and unlabeled polypeptides for binding to a limited quantity of antibodies.
  • Suitable radiolabels include, but are not limited to, I 125 .
  • a fixed concentration of I 125 -labeled polypeptide is incubated with a series of dilution of an antibody specific to the polypeptide. When the unlabeled polypeptide is added to the system, the amount of the I 125 -polypeptide that binds to the antibody is decreased.
  • a standard curve can therefore be constructed to represent the amount of antibody-bound I 125 -polypeptide as a function of the concentration of the unlabeled polypeptide. From this standard curve, the concentration of the polypeptide in unknown samples can be determined. Protocols for conducting RIA are well known in the art.
  • Suitable antibodies for the present invention include, but are not limited to, polyclonal antibodies, monoclonal antibodies, chimeric antibodies, humanized antibodies, single chain antibodies, Fab fragments, or fragments produced by a Fab expression library.
  • Neutralizing antibodies i.e., those which inhibit dimer formation
  • Methods for preparing these antibodies are well known in the art.
  • the antibodies of the present invention can bind to the corresponding prognosis gene products or other desired antigens with binding affinities of at least 10 4 M ⁇ 1 , 10 5 M ⁇ 1 , 10 6 M ⁇ 1 , 10 7 M ⁇ 1 , or more.
  • the antibodies of the present invention can be labeled with one or more detectable moieties to allow for detection of antibody-antigen complexes.
  • the detectable moieties can include compositions detectable by spectroscopic, enzymatic, photochemical, biochemical, bioelectronic, immunochemical, electrical, optical or chemical means.
  • the detectable moieties include, but are not limited to, radioisotopes, chemiluminescent compounds, labeled binding proteins, heavy metal atoms, spectroscopic markers such as fluorescent markers and dyes, magnetic labels, linked enzymes, mass spectrometry tags, spin labels, electron transfer donors and acceptors, and the like.
  • the antibodies of the present invention can be used as probes to construct protein arrays for the detection of expression profiles of the prognosis genes. Methods for making protein arrays or biochips are well known in the art.
  • a substantial portion of probes on a protein array of the present invention are antibodies specific for the prognosis gene products. For instance, at least 10%, 20%, 30%, 40%, 50%, or more probes on the protein array can be antibodies specific for the prognosis gene products.
  • the expression levels of the prognosis genes of are determined by measuring the biological functions or activities of these genes.
  • suitable in vitro or in vivo assays can be developed to evaluate the function or activity. These assays can be subsequently used to assess the level of expression of the prognosis gene.
  • Comparison between the expression profile of a patient of interest and the reference expression profile(s) can be conducted manually or electronically. In one example, comparison is carried out by comparing each component in one expression to the corresponding component in another expression profile.
  • the component can be the expression level of a prognosis gene, a ratio between the expression levels of two prognosis genes, or another measure capable of representing gene expression patterns.
  • the expression level of a gene can have an absolute or a normalized or relative value. The difference between two corresponding components can be assessed by fold changes, absolute differences, or other suitable means.
  • Comparison between expression profiles can also be conducted using pattern recognition or comparison programs, such as the k-nearest-neighbors algorithm as described in Armstrong, et al., supra, or the weighted voting algorithm as described below.
  • pattern recognition or comparison programs such as the k-nearest-neighbors algorithm as described in Armstrong, et al., supra, or the weighted voting algorithm as described below.
  • serial analysis of gene expression (SAGE) technology the GEMTOOLS gene expression analysis program (Incyte Pharmaceuticals), the GeneCalling and Quantitative Expression Analysis technology (Curagen), and other suitable methods, programs or systems can be used to compare expression profiles.
  • prognosis genes can be used in the comparison of expression profiles. For instance, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 30, 40, 50, or more prognosis genes can be used.
  • the prognosis gene(s) used in the comparison can be selected to have relatively small p-values (e.g., two-sided p-values). In one example, the p-values indicate the statistical significance of the difference between gene expression levels in different classes of patients. In another example, the p-values suggest the statistical significance of the correlation between gene expression patterns and clinical outcome.
  • the prognosis genes used in the comparison have p-values of no greater than 0.05, 0.01, 0.001, 0.0005, 0.0001, or less. Prognosis genes with p-values of greater than 0.05 can also be used. These genes may be identified, for instance, by using a relatively small number of blood samples.
  • Similarity or difference between the expression profile of a patient of interest and the reference expression profile(s) is indicative of the class membership of the patient of interest. Similarity or difference can be determined by any suitable means.
  • a component in a reference profile is a mean value, and the corresponding component in the expression profile of the patient of interest falls within the standard deviation of the mean value.
  • the expression profile of the patient of interest may be considered similar to the reference profile with respect to that particular component.
  • Other criteria such as a multiple or fraction of the standard deviation or a certain degree of percentage increase or decrease, can be used to measure similarity.
  • At least 50% (e.g., at least 60%, 70%, 80%, 90%, or more) of the components in the expression profile of the patient of interest are considered similar to the corresponding components in a reference profile.
  • the expression profile of the patient of interest may be considered similar to the reference profile.
  • Different components in the expression profile may have different weights for the comparison.
  • lower percentage thresholds e.g., less than 50% of the total components are used to determine similarity.
  • the prognosis gene(s) and the similarity criteria can be selected such that the accuracy of outcome prediction (the ratio of correct calls over the total of correct and incorrect calls) is relatively high.
  • the accuracy of prediction can be at least 50%, 60%, 70%, 80%, 90%, or more.
  • Prognosis genes with prediction accuracy of less than 50% can also be used, provided that the prediction is statistically significant.
  • the effectiveness of outcome prediction can also be assessed by sensitivity and specificity.
  • the prognosis genes and the comparison criteria can be selected such that both the sensitivity and specificity of outcome prediction are relatively high.
  • the sensitivity and specificity can be at least 50%, 60%, 70%, 80%, 90%, 95%, or more.
  • Prognosis genes having lower sensitivity or specificity can be used as long as the prediction is statistically significant.
  • gene expression-based outcome prediction can be combined with other clinical evidence or prognostic methods to improve the effectiveness or accuracy of outcome prediction.
  • the expression profile of a patient of interest is compared to at least two reference expression profiles.
  • the first reference expression profile can be prepared from peripheral blood samples of patients in a first outcome class
  • the second reference expression profile is prepared from peripheral blood samples of patients in a second outcome class.
  • Comparison between the expression profile of a patient of interest and two or more reference expression profiles can be performed by any suitable means.
  • the k-nearest-neighbors algorithm as described in Armstrong, et al., supra, is used.
  • the k-nearest-neighbors algorithm can effectively assign a patient to a clinical class.
  • the sensitivity and specificity of the assignment can be at least 50%, 60%, 70%, 80%, 90%, 95%, or more.
  • the effectiveness of assignment is evaluated based on leave-one-out cross validation.
  • the accuracy for leave-one-out cross validation can be, for instance, at least 50%, 60%, 70%, 80%, 90%, 95%, or more.
  • Prognosis genes or class predictors with low assignment sensitivity/specificity or leave-one-out cross validation accuracy, such as less than 50%, can also be used in the present invention.
  • a weighted voting algorithm is used.
  • the expression level of each gene in the classifier set contributes to an overall vote on the classification of the sample. See Slonim, et al., supra.
  • the prediction strength is a combined variable that indicates the support for one class or the other, and can vary between 0 (narrow margin of victory) and 1 (wide margin of victory) in favor of the predicted class. See Golub, et al., supra, and Slonim, et al., supra.
  • Software programs suitable for the weight voting analysis include, but are not limited to, GeneCluster 2 software. GeneCluster 2 software is available from MIT Center for Genome Research at Whitehead Institute (e.g., www-genome.wi.mit.edu/cancer/software/genecluster2/gc2.html).
  • a set of prognosis genes are selected to create a class predictor (classifier). Each gene in the class predictor casts a weighted vote for one of the two classes (class 0 and class 1).
  • a positive v g indicates a vote for class 0, and a negative v g indicates a vote for class 1.
  • V0 denotes the sum of all positive votes
  • V1 denotes the absolute value of the sum of all negative votes.
  • Cross-validation can be used to evaluate the accuracy of the class predictor created under the k-nearest-neighbors or weighted voting algorithm. Briefly, one sample which has been used to identify the prognosis genes under the neighborhood analysis is withheld. A class predictor is then created based on the remaining samples and used to predict the class of the sample withheld. This process can be repeated for each sample that has been used in the neighborhood analysis. Different class predictors can be evaluated using the cross-validation process, and the best class predictor with the most accurate predication can be identified.
  • Suitable prediction strength (PS) thresholds can be assessed by plotting the cumulative cross-validation error rate against the prediction strength. In one embodiment, a positive predication is made if the absolute value of PS for the sample of interest is no less than 0.3. Other PS thresholds, such as no less than 0.1, 0.2, 0.4 or 0.5, can also be used. In many embodiments, a threshold is selected such as the accuracy of prediction is optimized and the incidence of both false positive and false negative results is minimized.
  • the class predictor includes n prognosis genes identified under the neighborhood analysis. A half of these prognosis genes has the largest P(g,c) scores, and the other half has the largest ⁇ P(g,c) scores. The number n therefore is the only free parameter in defining the class predictor.
  • the prognosis genes or class predictors of the present invention can be used to assign a solid tumor patient of interest to an outcome class.
  • patients having the solid tumor can be divided into at least two classes.
  • the first class of patients has a first specified TTD (e.g., TTD of less than 150 days from initiation of a therapeutic treatment of the solid tumor), and the second class of patients has a second specified TTD (e.g., TTD of more than 550 days from initiation of the therapeutic treatment).
  • TTD e.g., TTD of less than 150 days from initiation of a therapeutic treatment of the solid tumor
  • TTD e.g., TTD of more than 550 days from initiation of the therapeutic treatment
  • Genes that are substantially correlated with the class distinction between these two classes of patients can be identified and used to assign the patient of interest to one of these two outcome classes.
  • all of the expression profiles used in the comparison are baseline profiles which are prepared from baseline peripheral blood samples isolated prior to a therapeutic treatment.
  • the first class of patients has a specified TTP (e.g., TTP of no less than 106 days from initiation of a therapeutic treatment), and the second class of patients has another specified TTP (e.g., TTP of less than 106 days from initiation of the therapeutic treatment).
  • TTP e.g., TTP of no less than 106 days from initiation of a therapeutic treatment
  • TTP e.g., TTP of less than 106 days from initiation of the therapeutic treatment
  • the solid tumor can be RCC
  • the therapeutic treatment can be a CCI-779 therapy.
  • the prognosis gene(s) can be selected from, for instance, Table 13.
  • the first class of patients includes or consists of patients having the lowest quartile of TTP among a population of patients who have the same solid tumor and are subject to the same therapeutic treatment.
  • the second class of patients includes or consists of patients having the highest quartile of TTP among the population of patients.
  • the solid tumor can be RCC
  • the therapeutic treatment can be a CCI-779 therapy.
  • the prognosis gene(s) can be selected from, for instance, Table 12.
  • the first class of patients includes or consists of patients having the lowest quartile of TTD among a population of patients who have the same solid tumor and are subject to the same therapeutic treatment
  • the second class of patients includes or consists of patients having the highest quartile of TTD among the population of patients.
  • the solid tumor can be RCC
  • the therapeutic treatment can be a CCI-779 therapy.
  • the first class of patients has a prognosis determined by a risk assessment method
  • the second class of patients has another prognosis determined by the same risk assessment method.
  • both classes of patients have RCC
  • the risk assessment method is based on Motzer risk classification.
  • Motzer risk classification RCC patients can have poor, intermediate, or favorable prognoses.
  • one class of RCC patients has poor prognosis, and the other class of RCC patients has intermediate prognosis.
  • the prognosis gene(s) can be selected from, for instance, Table 11.
  • the first class of patients has progressive disease after a specified time of treatment
  • the second class of patients has non-progressive disease (such as complete response, partial response, minor response, or stable disease) after the same specified time of treatment.
  • patients having the solid tumor can be clustered into at least two classes based on their gene expression profiles in PBMCs. Suitable algorithms for this purpose include, but are not limited to, unsupervised clustering analyses. Each of the two classes can be associated with a different respective clinical outcome. For instance, the majority of one class of patients can have a specified TTD (e.g., TTD of less than 365 days), while the majority of the other class of patients can have another specified TTD (e.g., TTD of no less than 365 days). Genes that are substantially correlated with the class distinction between these two classes can be identified. These genes, or the class predictors derived therefrom, can be used to predict the class membership of a patient of interest.
  • the solid tumor is RCC
  • the therapeutic treatment is a CCI-779 therapy.
  • the prognosis gene(s) can be selected from, for instance, Table 16.
  • Prognosis genes or class predictors that are capable of distinguishing three or more different outcome classes can also be employed in the present invention. These prognosis genes can be identified using multi-class correlation metrics. Suitable programs for carrying out multi-class correlation analysis include, but are not limited to, GeneCluster 2 software (MIT Center for Genome Research at Whitehead Institute, Cambridge, Mass.). Under the analysis, patients having the solid tumor can be divided into at least three classes, and each class has a different respective clinical outcome. The prognosis genes identified under multi-class correlation analysis are differentially expressed in PBMCs of one class of patients relative to PBMCs of other classes of patients. In one embodiment, the identified prognosis genes are substantially correlated with a class distinction between the multiple classes. For instance, the prognosis genes can be selected from those above the 1%, 5%, 10%, 25%, or 50% significance level under a permutation test.
  • the expression profile of the prognosis gene(s) used in the comparison is correlated with clinical outcome of reference patients under a statistical method.
  • Suitable statistical methods for this purpose include, but are not limited to, Spearman's rank correlation, Cox proportional hazard regression model, or other rank tests or survival models.
  • the reference patients have the same solid tumor as the patient of interest, and the clinical outcome of the reference patients is either known or determinable.
  • clinical outcome of the patient of interest can be predicted. For instance, if the expression profile of the patient of interest is more similar to the expression profile of one particular reference patient as compared to other reference patients, clinical outcome of that particular reference patient can be indicative of clinical outcome of the patient of interest.
  • prognosis genes can be used for outcome prediction based on statistical methods.
  • one prognosis gene is used.
  • the reference patient whose expression profile is most similar to that of the patient of interest can be identified. A prediction that clinical outcome of the patient of interest is most analogous to that of the reference patient can therefore be made.
  • two or more prognosis genes are used.
  • the expression profile of the patient of interest and the reference expression profile can be compared by a pattern recognition or comparison algorithm.
  • the Euclidean distance is used to measure the similarity between two different expression profiles.
  • time-associated clinical outcome indicator can be evaluated based on statistical methods.
  • time-associated clinical outcomes include, but are not limited to, TTP and TTD.
  • outcome prediction is based on Spearman's correlation test.
  • the patient of interest and the reference patients have RCC and are being treated by a CCI-779 therapy.
  • clinical outcome is measured by TTP, and the prognosis gene(s) is selected from Tables 6a and 6b.
  • clinical outcome is measured by TTD, and the prognosis gene(s) is selected from Tables 6c and 6d.
  • the relative risk for TTD or TTP can be qualitatively assessed based on the peripheral blood expression level of a prognosis gene in the patient of interest, in conjunction with the correlation coefficient of the prognosis gene.
  • outcome prediction is based on Cox proportional hazard regression model.
  • the patient of interest and the reference patients have RCC and are being treated by a CCI-779 therapy.
  • clinical outcome is measured by TTP, and the prognosis gene(s) is selected from Tables 9a and 9b.
  • clinical outcome is measured by TTD, and the prognosis gene(s) is selected from Tables 9c and 9d.
  • the relative risk for TTD or TTP can be qualitatively assessed based on the peripheral blood expression level of a prognosis gene in the patient of interest, in light of the hazard ratio of the prognosis gene.
  • the present invention provides electronic systems useful for the prognosis or selection of treatment of RCC and other solid tumors.
  • These systems include input or communication devices for receiving the expression profile of the patient of interest as well as the reference expression profile(s).
  • the reference expression profile(s) can be stored in a database or another medium.
  • the reference expression profile(s) is readily retrievable or modifiable.
  • the comparison between expression profiles can be conducted electronically, such as through a processor or a computer.
  • the processor or computer can execute one or more programs to compare the expression profile of the patient of interest to the reference expression profile(s).
  • the program(s) can be stored in a memory or downloaded from another source, such as an internet server.
  • the program(s) includes a k-nearest-neighbors or weighted voting algorithm.
  • the electronic system is coupled to a nucleic acid array and can receive or process expression data generated by the nucleic acid array.
  • kits useful for the prognosis or selection of treatment of solid tumors include probes/primers for detecting expression patterns of one or more solid tumor prognosis genes. Each prognosis gene is differentially expressed in PBMCs of patients who have different clinical outcomes.
  • the probe/primers can hybridize under stringent or nucleic acid array hybridization conditions to the RNA transcripts, or the complements thereof, of the corresponding prognosis genes. Hybridization or amplification agents can be included in the kits.
  • kits of the present invention can include any number of probes/primers.
  • each kit includes at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or more different probes/primers, and each of these different probes/primers can hybridize under stringent conditions or nucleic acid array hybridization conditions to a different respective solid tumor prognosis gene.
  • the solid tumor to be prognosed can be RCC, and the prognosis genes can be selected from Tables 6a, 6b, 6c, 6d, 9a, 9b, 9c, 9d, 10, 11, 12, 13, 16, 20 and 21.
  • kits of the present invention include one or more antibodies capable of binding to the polypeptides encoded by respective solid tumor prognosis genes.
  • the antibodies can be, without limitation, polyclonal, monoclonal, single-chain, or humanized.
  • the antibodies can bind to the respective polypeptide products with affinities of at least 10 5 M ⁇ 1 , 10 6 M ⁇ 1 , 10 7 M ⁇ 1 , or more.
  • the kits of the present invention include at least 2, 3, 4, 5, 10, 15, 20, or more different antibodies, and each of these different antibodies is capable of binding to a polypeptide encoded by a different respective RCC prognosis gene.
  • the kits of the present invention can also include immunoassay reagents, such as secondary antibodies, controls, or enzyme substrates.
  • the probes or antibodies of the present invention can be either labeled or unlabeled.
  • Labeled antibodies can be detectable by spectroscopic, photochemical, biochemical, bioelectronic, immunochemical, electrical, optical, chemical, or other suitable means.
  • Exemplary labeling moieties for an antibody include radioisotopes, chemiluminescent compounds, labeled binding proteins, heavy metal atoms, spectroscopic markers, such as fluorescent markers and dyes, magnetic labels, linked enzymes, mass spectrometry tags, spin labels, electron transfer donors and acceptors, and the like.
  • the probes or antibodies of the present invention can be enclosed in a vial, a tube, a bottle, a box, or another holding means.
  • the probes or antibodies are stably attached to one or more substrate supports.
  • Nucleic acid hybridization or immunoassays can be directly carried out on the substrate support(s).
  • Suitable substrate supports include, but are not limited to, glasses, silica, ceramics, nylons, quartz wafers, gels, metals, papers, beads, tubes, fibers, films, membranes, column matrixes, or microtiter plate wells.
  • the present invention allows for personalized treatment of RCC or other solid tumors.
  • Numerous treatment options or regimes can be analyzed by the present invention.
  • Prognosis genes for each treatment can be determined.
  • the peripheral blood expression profiles of these prognosis genes in a patient of interest can be analyzed to identify treatments that have favorable prognoses for the patient of interest.
  • a “favorable” prognosis is a prognosis which is better than the average prognosis for all available treatments of the solid tumor.
  • RCC can be treated by drug therapies.
  • Suitable drugs include cytokines, such as interferon or interleukin 2, and chemotherapy drugs, such as CCI-779, AN-238, vinblastine, floxuridine, 5-fluorouracil, or tamoxifen.
  • AN238 is a cytotoxic agent which has 2-pyrrolinodoxorubicin linked to a somatostatin (SST) carrier octapeptide.
  • SST somatostatin
  • AN238 can be targeted to SST receptors on the surface of RCC tumor cells.
  • Chemotherapy drugs can be used individually or in combination with other drugs, cytokines, or therapies.
  • monoclonal antibodies, antiangiogenesis drugs, or anti-growth factor drugs can be employed to treat RCC.
  • RCC treatment can also be surgical. Suitable surgical choices include, but are not limited to, radical nephrectomy, partial nephrectomy, removal of metastases, arterial embolization, laparoscopic nephrectomy, cryoablation, and nephron-sparing surgery. Moreover, radiation, gene therapy, immunotherapy, adoptive immunotherapy, or any other conventional or experimental therapy can be used.
  • prostate cancer treatments include, but are not limited to, radiation therapy, hormonal therapy, and cryotherapy.
  • the present invention contemplates any novel or experimental treatment of solid tumors.
  • Prognosis genes or class predictors for each treatment of a solid tumor can be identified according to the present invention. Treatments with favorable prognoses for a patient of interest can therefore be determined. Treatment selection can be conducted manually or electronically. In one embodiment, a reference expression profile database is established for each treatment and each prognosis gene.
  • prognosis gene may be affected by the disease stage of a solid tumor. For instance, prognosis genes can be identified from patients at a particular disease stage. Genes thus identified may be more effective in predicting clinical outcome of a patient of interest who is also at that disease stage.
  • Disease stages may also affect treatment selection. For instance, for RCC patients in stages I or II, radical or partial nephrectomy is commonly selected. For RCC patients in stage III, radical nephrectomy is among the preferred treatments. For RCC patients in stage IV, cytokine immunotherapy, combined immunotherapy and chemotherapy, or other drug therapies can be employed. Therefore, the disease stage of a patient of interest can be used to assist the gene expression-based selection for a favorable treatment of the patient.
  • PBMCs Prior to initiation of therapy, whole blood samples (8 mL) were collected into Vacutainer sodium citrate cell purification tubes (CPTs) and PBMCs were isolated according to the manufacturer's protocol (Becton Dickinson). All blood samples were shipped in CPTs overnight prior to PBMC processing. PBMCs were purified over Ficoll gradients, washed two times with PBS and counted. Total RNA was isolated from PBMC pellets using the RNeasy mini kit (Qiagen, Valencia, Calif.). Labeled target for oligonucleotide arrays was prepared using a modification of the procedure described in Lockhart, et al., N ATURE B IOTECHNOLOGY, 14:1675-80 (1996).
  • RNA 2 ⁇ g total RNA was converted to cDNA by priming with an oligo-dT primer containing a T7 DNA polymerase promoter at the 5′ end.
  • the cDNA was used as the template for in vitro transcription using a T7 DNA polymerase kit (Ambion, Woodlands, Tex.) and biotinylated CTP and UTP (Enzo). Labeled cRNA was fragmented in 40 mM Tris-acetate pH 8.0, 100 mM KOAc, 30 mM MgOAc for 35 minutes at 94° C. in a final volume of 40 ⁇ l.
  • the sensitivity of detection of the arrays ranged between about 1:300,000 and 1:100,000 copies/million.
  • Labeled probes were denatured at 99° C. for 5 minutes and then 45° C. for 5 minutes and hybridized to oligonucleotide arrays comprised of over 12,500 human genes (HgU95A, Affymetrix). Arrays were hybridized for 16 hours at 45° C.
  • the hybridization buffer was comprised of 100 mM MES, 1 M [Na + ], 20 mM EDTA, and 0.01% Tween 20. After hybridization, the cartridges were washed extensively with wash buffer (6 ⁇ SSPET), for instance, three 10-minute washes at room temperature. These hybridization and washing conditions are collectively referred to as “nucleic acid array hybridization conditions.” The washed cartridges were then stained with phycoerythrin coupled to streptavidin.
  • 12 ⁇ MES stock contains 1.22 M MES and 0.89 M [Na + ].
  • the stock can be prepared by mixing 70.4 g MES free acid monohydrate, 193.3 g MES sodium salt and 800 ml of molecular biology grade water, and adjusting volume to 1000 ml.
  • the pH should be between 6.5 and 6.7.
  • 2 ⁇ hybridization buffer can be prepared by mixing 8.3 ml of 12 ⁇ MES stock, 17.7 mL of 5 M NaCl, 4.0 mL of 0.5 M EDTA, 0.1 mL of 10% Tween 20 and 19.9 mL of water.
  • 6 ⁇ SSPET contains 0.9 M NaCl, 60 mM NaH 2 PO 4 , 6 mM EDTA, pH 7.4, and 0.005% Triton X-100.
  • the wash buffer can be replaced with a more stringent wash buffer. 1000 ml stringent wash buffer can be prepared by mixing 83.3 mL of 12 ⁇ MES stock, 5.2 mL of 5 M NaCl, 1.0 mL of 10% Tween 20 and 910.5 mL of water.
  • GENECHIP 3.2 software uses algorithms to calculate the likelihood as to whether a gene is “absent” or “present” as well as a specific hybridization intensity value or “average difference” for each transcript represented on the array. For instance, “present” calls are calculated by estimating whether a transcript is detected in a sample based on the strength of the gene's signal compared to background. The algorithms used in these calculations are described in the Affymetrix GeneChip Analysis Suite User Guide (Affymetrix). The “average difference” for each transcript was normalized to “frequency” values according to the procedures of Hill, et al., S CIENCE, 290: 809-812 (2000).
  • transcripts were evaluated further if they met the following criteria.
  • genes that were designated “absent” by the GENECHIP 3.2 software in all samples were excluded from the analysis.
  • a fourth criterion which requires that average fold changes in frequency values across the statistically significant subset of genes be 2-fold or greater, was also used.
  • Unsupervised hierarchical clustering of genes was performed using the procedure described in Eisen, et al., supra. Nearest-neighbor prediction analysis and supervised cluster analysis was performed using metrics illustrated in Golub, et al., supra.
  • data were log transformed and normalized to have a mean value of zero and a variance of one.
  • a Student's t-test was used to compare PBMC expression profiles in different outcome classes. In the comparisons, a p value ⁇ 0.05 can be used to indicate statistical significance.
  • transcripts meeting a more stringent data reduction filter were used (at least 25% present calls, and an average frequency across all 45 RCC PBMCs ⁇ 5 ppm). This more stringent filter was used to avoid the inclusion low level transcripts in the predictive models.
  • For nearest-neighbor analysis all expression data in training sets and test sets were log transformed prior to analysis. In training sets of data, models containing increasing numbers of features (transcript sequences) were built using a two-sided approach (equal numbers of features in each class) with a S2N similarity metric that used median values for the class estimate. All comparisons were binary distinctions, and each model (with increasing numbers of features) was evaluated by leave one out cross validation.
  • Tables 18 and 19 demonstrate the distributions of the various cell subtypes (neutrophils, eosinophils, lymphocytes and monocytes) between PBMCs of patients assigned to either good or poor outcome categories for TTP and survival.
  • the mean percentages and the p-value for a t-test (unequal variance) between the good and poor outcome PBMC profiles for each cell subtype are presented.
  • the first analysis is summarized for the comparison of short- and long-term survivors (less than or greater than one year survival) in FIGS. 6A, 6B , and 6 C.
  • Patients were stratified as described above into two groups based upon TTD less than or greater than 365 days.
  • a GeneCluster analysis using the signal-to-noise metric identified transcripts correlated with these groups of patients ( FIG. 6A ).
  • Predictive gene classifiers containing between 2 and 60 genes in steps of 2 (and 60-200 genes in steps of 10) were evaluated by leave-one-out cross validation to identify the smallest predictive model yielding the most accurate class assignments of short- and long-term survivors in the training set.
  • the best model found was a classifier of 20 genes ( FIG. 6B and Table 20). This predictive model was then evaluated using a nearest-neighbors approach on the remaining test set of samples ( FIG. 6C ). This entire approach was repeated for the stratification of short vs long-term TTP as illustrated in FIGS. 7A, 7B , and 7 C.
  • the best model found was a classifier of 30 genes ( FIG. 7B and Table 21), and this predictive model was also evaluated using a nearest-neighbors approach on the remaining test set of samples ( FIG. 7C ).
  • the circulating monocytes, T cells and B cells may serve as a sensitive monitor of the organism's physiological state.
  • T cells and B cells or activated neutrophils passing through CPT
  • a complex transcriptional response measured through profiling As these cells pass through various tissues, their reaction to the microenvironment is captured in a complex transcriptional response measured through profiling.
  • such patterns appear to not only be diagnostic of disease state (e.g., RCC) but may also reflect differential responses to variations in the clinically same disease state (e.g., advanced RCC with different degrees of aggressiveness).
  • the PBMCs due to their transit through the body, may serve as an accessible surrogate monitor of tissues and systems that are not easily obtained by routine biopsies.
  • transcripts elevated in PBMCs of patients with shorter TTP or survival include those involved in cytoskeletal organization/cell motility, associated small GTPases, general pathways of proteasome-dependent catabolism and general pathways of metabolism.
  • transcripts elevated in PBMCs of patients with longer TTP or survival included those involved in mRNA transport, mRNA processing/splicing and ribosomal protein subunits.
  • Similar surrogate tissue analyses can be used to identify transcriptional profiles that are specific to a particular therapy in question (e.g., CCI-779, interferon-alpha (IFN- ⁇ ), or CCI-779+IFN- ⁇ ), as well as those that are simply prognostic of disease outcome regardless of therapy.
  • a particular therapy in question e.g., CCI-779, interferon-alpha (IFN- ⁇ ), or CCI-779+IFN- ⁇

Abstract

Solid tumor prognosis genes, and methods, systems and equipment of using these genes for the prognosis and treatment of solid tumors. Prognosis genes for a solid tumor can be identified by the present invention. The expression profiles of these genes in peripheral blood mononuclear cells (PBMCs) are correlated with clinical outcome of the solid tumor. The prognosis genes of the present invention can be used as surrogate markers for predicting clinical outcome of a solid tumor in a patient of interest. These genes can also be used to select a treatment which has a favorable prognosis for the solid tumor of the patient of interest.

Description

    CROSS-REFERENCE TO RELATED APPLICATIONS
  • The present application is a continuation of U.S. application Ser. No. 10/834,268, filed on Apr. 29, 2004, which claims the benefit of U.S. Provisional Application No. 60/466,067, filed Apr. 29, 2003, and U.S. Provisional Application No. 60/538,246, filed Jan. 23, 2004, the disclosures of each of which are hereby incorporated by reference in their entireties.
    • REFERENCE TO SEQUENCE LISTING AND TABLES ON COMPACT DISC
  • This application includes as part of the originally filed subject-matter two compact discs, labeled “Copy 1 CD Containing Sequence Listing and Large Tables” and “Copy 2 CD Containing Sequence Listing and Large Tables.” Each compact disc includes the following files: “Sequence Listing.ST25.txt” (5,454 KB, created Mar. 8, 2007), “Table 3—Spearman Correlation of Baseline Expression with Clinical Outcome.txt” (298 KB, created Jan. 19, 2004), “Table 4—Qualifiers and the Corresponding Entrez and Unigene Accession Nos.txt” (179 KB, created Jan. 20, 2004), “Table 5—Genes and Gene Titles.txt” (331 KB, created Jan. 21, 2004), and “Table 8—Cox Regression of Clinical Outcome on Baseline Gene Expression.txt” (294 KB, created Jan. 19, 2004). The contents of the compact discs labeled “Copy 1 CD Containing Sequence Listing and Large Tables” and “Copy 2 CD Containing Sequence Listing and Large Tables” are hereby incorporated by reference herein in their entireties.
    • TECHNICAL FIELD
  • The present invention relates to solid tumor prognosis genes and methods of using these genes for the prognosis or treatment of solid tumors.
    • BACKGROUND
  • Expression profiling studies in primary tissues have demonstrated that there exist transcriptional differences between normal and malignant tissues. See, for example, Su, et al., CANCER RES, 61:7388-7393 (2001); and Ramaswamy, et al., PROC NATL ACAD SCI U.S.A., 98:15149-15151 (2001). Recent clinical analyses have also identified expression profiles within tumors that appear to be highly correlated with certain measures of clinical outcomes. One study has demonstrated that expression profiling of primary tumor biopsies yields prognostic “signatures” that rival or may even out-perform currently accepted standard measures of risk in cancer patients. See van de Vijver, et al., N ENGL J MED, 347:1999-2009 (2002).
    • SUMMARY OF THE INVENTION
  • The present invention provides methods, systems and equipment for prognosis or selection of treatment of solid tumors. Prognosis genes for a solid tumor can be identified by the present invention. The expression profiles of these genes in peripheral blood mononuclear cells (PBMCs) are correlated with clinical outcome of the solid tumor. These genes can be used as surrogate markers for predicting clinical outcome of the solid tumor in a patient of interest. These genes can also be used to identify or select treatments which have favorable prognoses for the patient of interest.
  • In one aspect, the present invention provides methods that are useful for the prognosis or selection of treatment of a solid tumor in a patient of interest. The methods include comparing an expression profile of one or more prognosis genes in a peripheral blood sample of the patient of interest to at least one reference expression profile of the prognosis genes. Each of the prognosis genes is differentially expressed in PBMCs of a first class of patients as compared to PBMCs of a second class of patients. Both classes of patients have a solid tumor, and each class of patients has a different clinical outcome. In many embodiments, the prognosis genes are substantially correlated with a class distinction between the two classes of patients.
  • Solid tumors amenable to the present invention include, but are not limited to, renal cell carcinoma (RCC), prostate cancer, head/neck cancer, and other tumors that do not have their origin in blood or lymph cells.
  • Clinical outcome can be measured by any clinical indicator. In one embodiment, clinical outcome is determined based on clinical classifications such as complete response, partial response, minor response, stable disease, progressive disease, non-progressive disease, or any combination thereof. In another embodiment, clinical outcome is measured by time to disease progression (TTP) or time to death (TTD). In still another embodiment, clinical outcome is prognosticated by using traditional risk assessment methods, such as Motzer risk classification for RCC. Other patient responses to a therapeutic treatment can also be used to measure clinical outcome. Examples of solid tumor treatments include, but are not limited to, drug therapy (e.g., CCI-779 therapy), chemotherapy, hormone therapy, radiotherapy, immunotherapy, surgery, gene therapy, anti-angiogenesis therapy, palliative therapy, or any combination thereof.
  • In many embodiments, the reference expression profile(s) includes an average expression profile of the prognosis genes in peripheral blood samples of reference patients. In many instances, the reference patients have the same solid tumor as the patient of interest, and the clinical outcome of the reference patients are either known or determinable.
  • The peripheral blood samples of the patient of interest and reference patients can be whole blood samples, or blood samples comprising enriched or purified PBMCs. Other types of blood samples can also be employed in the present invention. In one embodiment, all of the peripheral blood samples are baseline samples which are isolated from respective patients prior to a therapeutic treatment of the patients.
  • Any comparison method can be used to compare the expression profile of the patient of interest to the reference expression profile(s). In one embodiment, the comparison is based on the absolute or relative peripheral blood expression level of each prognosis gene. In another embodiment, the comparison is based on the ratios between expression levels of two or more prognosis genes. In yet another embodiment, the reference expression profiles include at least two distinct expression profiles, each being derived from a different class of reference patients. The comparison of the expression profile of the patient of interest to the reference expression profiles can be carried out by using methods including, but not limited to, hierarchical clustering, k-nearest-neighbors, or weighted-voting algorithm.
  • In still another embodiment, the methods of the present invention include selecting a treatment which has a favorable prognosis for the solid tumor in the patient of interest.
  • In another aspect, the present invention provides other methods useful for the prognosis or selection of treatment of a solid tumor in a patient of interest. These methods include comparing an expression profile of one or more prognosis genes in a peripheral blood sample of the patient of interest to at least one reference expression profile of the prognosis genes, where each of the prognosis genes is differentially expressed in PBMCs of a first class of patients as compared to PBMCs of a second class of patients. Each of the first and second classes is a subcluster formed by an unsupervised clustering analysis of gene expression profiles in PBMCs of patients who have the solid tumor. In one embodiment, the majority of the first class of patients has a first clinical outcome, and the majority of the second class of patients has a second clinical outcome.
  • In yet another aspect, the present invention further provides methods useful for the prognosis or selection of treatment of a solid tumor in a patient of interest. The methods include comparing an expression profile of one or more prognosis genes in a peripheral blood sample of the patient of interest to at least one reference expression profile of the prognosis genes, where the expression levels of each of the prognosis genes in PBMCs of patients having the solid tumor are correlated with clinical outcomes of these patients. The association between PBMC expression levels and clinical outcome can be determined by a statistical method (e.g., Spearman's rank correlation or Cox proportional hazard regression model) or a class-based correlation metric (e.g., neighborhood analysis). In one embodiment, the solid tumor is RCC, and clinical outcome is measured by patient response to a CCI-779 therapy. In another embodiment, the prognosis genes include at least one gene selected from Tables 6a, 6b, 6c, 6d, 9a, 9b, 9c, 9d, 10, 11, 12, 13, 16, 20, and 21.
  • The present invention also features systems useful for the prognosis or selection of treatment of a solid tumor in a patient of interest. The systems include (1) a memory or a storage medium comprising data that represent an expression profile of one or more prognosis genes in a peripheral blood sample of the patient of interest, (2) a storage medium comprising data that represent at least one reference expression profile of the prognosis genes, (3) a program capable of comparing the expression profile of the patient of interest to the reference expression profile, and (4) a processor capable of executing the program. The expression levels of the prognosis genes in PBMCs of patients having the solid tumor are correlated with clinical outcomes of the patients.
  • Moreover, the present invention features nucleic acid or protein arrays useful for the prognosis or selection of treatment of a solid tumor in a patient of interest. The nucleic acid or protein arrays include concentrated probes for solid tumor prognosis genes.
  • Other features, objects, and advantages of the present invention are apparent in the detailed description that follows. It should be understood, however, that the detailed description, while indicating embodiments of the present invention, is given by way of illustration only, not limitation. Various changes and modifications within the scope of the invention will become apparent to those skilled in the art from the detailed description.
    • BRIEF DESCRIPTION OF THE DRAWINGS
  • The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee. The drawings are provided for illustration, not limitation.
  • FIG. 1A depicts expression profiles of class-correlated genes identified by nearest-neighbor analysis of patients with survival of less than 150 days versus patients with survival of greater than 550 days. The relative expression levels of the class-correlated genes (rows) are indicated for each patient (columns) according to the normalized expression level scale.
  • FIG. 1B shows the comparison of the signal to noise (S2N) similarity metric scores for class-correlated genes identified in FIG. 1A relative to S2N scores for the top 1%, 5%, and 50% of scores for class-correlated genes resulting from randomly permuted data sets.
  • FIG. 1C illustrates training set cross validation results for predictor gene sets of increasing size. Each predictor set was evaluated by cross validation to identify the predictor set with the highest accuracy for classification of the samples. In these analyses, a 58 gene predictor set (77% accuracy) was the optimal classifier.
  • FIG. 1D demonstrates cross validation results for each sample using the 58-gene predictor identified in FIG. 1C. A leave-one-out cross validation was performed and the prediction strengths were calculated for each sample in the analysis. For the purposes of illustration, confidence scores accompanying calls of “TTD>550 days” were assigned positive values, while prediction strengths accompanying calls of “TTD<150 days” were assigned negative values.
  • FIG. 2A shows the relative gene expression levels of a 42-gene classifier for the comparison of patients with intermediate versus poor Motzer risk classification.
  • FIG. 2B shows the relative gene expression levels for an 18-gene classifier identified in the comparison of patients with progressive disease versus any other clinical response.
  • FIG. 2C demonstrates the relative gene expression levels for a 6-gene classifier identified in the comparison of patients in the lower versus upper quartiles of time to disease progression.
  • FIG. 2D shows the relative gene expression levels for a 52-gene classifier identified in the comparison of patients in the lower versus upper quartiles of survival/time to death.
  • FIG. 2E depicts the relative expression levels for a 12-gene classifier identified in the comparison of patients with early (time to disease progression<106 days) versus all other times to disease progression (TTP≧106 days).
  • FIG. 3A illustrates the dendrogram of an unsupervised hierarchical clustering of baseline PBMC profiles in 45 RCC patients using all expressed genes present in at least one sample and possessing a frequency of greater than 10 ppm in at least one sample (5,424 genes total). PBMC expression profiles in the poor prognosis cluster are indicated by subcluster “A,” where 9 out of 12 patients with PBMC profiles in this subcluster exhibited survival of less than a year. PBMC expression profiles in the good prognosis cluster are indicated by subcluster “C,” where 10 out of 12 patients with PBMC profiles in this subcluster exhibited survival of greater than a year. The median survival for patients in subclusters A, B, C, and D is 281 days, 566 days, 573 days, and 502 days, respectively.
  • FIG. 3B shows baseline expression profiles of selected genes in RCC patients. The dendrogram of sample relatedness is indicated.
  • FIG. 4A illustrates the Kaplan-Meier survival curve for patients in the poor and good prognosis subclusters segregated on the basis of gene expression pattern.
  • FIG. 4B illustrates the Kaplan-Meier survival curve for patients in the poor and good prognosis subclusters segregated on the basis of Motzer risk assessment.
  • FIG. 5A demonstrates the result of supervised identification of a gene classifier for assigning class membership to patients in the good and poor prognosis subclusters. The relative expression levels of the most class-correlated gene (rows) are indicated for each patient (columns) according to the scale described in FIG. 1A.
  • FIG. 5B shows cross validation results for each sample using the gene classifier of FIG. 5A. A leave-one-out cross validation was performed and the confidence scores were calculated for each sample in the analysis. Similar to FIG. 1D, for the purposes of illustration, prediction strengths accompanying calls of “survival>1 year” were assigned positive values, while prediction strengths accompanying calls of “survival<1 year” were assigned negative values. Asterisks identify the false positives in this clinical assay designed to identify short survival times, and arrowheads indicate false negatives.
  • FIG. 6A shows the optimal gene classifier for year-long survival identified by nearest-neighbor analysis using a more stringent filter (at least 25% present calls, and an average frequency no less than 5 ppm). A GeneCluster gene selection approach identifies genes distinguishing patients with survival less than 365 days versus patients with survival greater than 365 days in the training set. The relative expression levels of the most class-correlated genes (rows) are indicated for each of the patients in the training set (columns) according to the scale described in FIG. 1A.
  • FIG. 6B evaluates prediction accuracy of gene classifiers of increasing size. Accuracy of class assignment for gene classifiers containing between 2 and 60 genes in steps of 2, and 60-200 genes in steps of 10, were evaluated by leave-one-out cross validation on the training set of samples. The smallest predictive model with the highest accuracy was selected (20 gene predictor, indicated by the arrow).
  • FIG. 6C demonstrates the result of evaluation of the optimal predictive model of FIG. 6B on an untested set of RCC PBMC profiles. A k-nearest-neighbors algorithm using the 20 gene classifier was used to assign class membership to the remaining 14 PBMC profiles, and the prediction strengths associated with the class assignments are presented for each sample in the analysis. For the purposes of illustration, confidence scores accompanying calls of “TTD<365 days” were assigned positive values, while confidence scores accompanying calls of “TTD>365 days” were assigned negative values. The overall accuracy of the gene classifier was 72%. By defining the clinical assay as the identification of favorable outcome, eight of eight patients with favorable outcome were correctly identified as having survival greater than one year (positive predictive value of 100%).
  • FIG. 7A illustrates the optimal gene classifier for greater than 106 day time to progression identified by nearest-neighbor analysis using a more stringent filter (at least 25% present calls, and an average frequency no less than 5 ppm). A GeneCluster gene selection approach identifies genes distinguishing patients with TTP less than 106 days versus patients with TTP greater than 106 days in the training set. The relative expression levels of the most class-correlated genes (rows) are indicated for each of the patients in the training set (columns) according to the scale of FIG. 1A.
  • FIG. 7B indicates prediction accuracy of gene classifiers of increasing size. Accuracy of class assignment for gene classifiers containing between 2 and 60 genes in steps of 2, and 60-200 genes in steps of 10, were evaluated by leave-one-out cross validation on the training set of samples. The smallest predictive model with the highest accuracy was selected (30 gene predictor, indicated by the arrow).
  • FIG. 7C shows the result of evaluation of the optimal predictive model of FIG. 7B on an untested set of RCC PBMC profiles. A k-nearest-neighbors algorithm using the 30 gene classifier was used to assign class membership to the remaining 14 PBMC profiles, and the prediction strengths associated with the class assignments are presented for each sample in the analysis. For the purposes of illustration, confidence scores accompanying calls of “TTP<106 days” were assigned positive values, while confidence scores accompanying calls of “TTD>106 days” were assigned negative values. The overall accuracy of the gene classifier was 85%. By defining the clinical assay as the identification of favorable outcome, eight of ten patients with favorable outcome were correctly identified as having TTP greater than one 106 days (positive predictive value of 80%) and three of three patients with poor outcome were correctly predicted to have TTP less than 106 days (negative predictive value 100%).
    • DETAILED DESCRIPTION
  • The present invention provides methods that are useful for prognosis or selection of treatment of solid tumors. These methods employ prognosis genes that are differentially expressed in peripheral blood samples of solid tumor patients who have different clinical outcomes. In many embodiments, the peripheral blood expression profiles of these prognosis genes are correlated with patients' clinical outcome or prognosis under a statistical method or a correlation model. In many other embodiments, solid tumor patients can be divided into at least two classes based on patients' clinical outcome or prognosis, and the prognosis genes are substantially correlated with a class distinction between these two classes of patients under a neighborhood analysis.
  • The prognosis genes of the present invention can be used as surrogate markers for the prediction of clinical outcome of solid tumors. The prognosis genes of the present invention can also be used for the identification of optimal treatments of solid tumors. Different patients may have distinct clinical responses to a therapeutic treatment due to individual heterogeneity of the molecular mechanism of the disease. The identification of gene expression patterns that correlate with patient response allows clinicians to select treatments based on predicted patient responses and thereby avoid adverse reactions. This provides improved power and safety of clinical trials and increased benefit/risk ratio for drugs and other therapeutic treatments. Peripheral blood is a tissue that can be routinely obtained from patients in a minimally invasive manner. By determining the correlation between patient outcome and gene expression profiles in peripheral blood samples, the present invention represents a significant advance in clinical pharmacogenomics and solid tumor treatment.
  • Various aspects of the invention are described in further detail in the following subsections. The use of subsections is not meant to limit the invention. Each subsection may apply to any aspect of the invention. In this application, the use of “or” means “and/or” unless stated otherwise.
  • I. General Methods for Identifying Solid Tumor Prognosis Genes
  • Previous studies demonstrated that baseline expression profiles in PBMCs from solid tumor patients were significantly distinct from those of disease-free subjects. See U.S. Provisional Application Ser. No. 60/459,782, filed Apr. 3, 2003, U.S. Provisional Application Ser. No. 60/427,982, filed Nov. 21, 2002, and U.S. patent application Ser. No. 10/717,597, filed Nov. 21, 2003, all of which are incorporated herein by reference. Studies also showed that gene expression profiles in PBMCs were predictive of anti-cancer drug activity in vivo. See U.S. Provisional Application Ser. No. 60/446,133, filed Feb. 11, 2003, and U.S. patent application Ser. No. 10/775,169, filed Feb. 11, 2004, both of which are incorporated herein by reference. In addition, studies indicated that PBMC baseline expression profiles were correlated with clinical outcomes of RCC or other non-blood diseases. See U.S. Provisional Application Ser. No. 60/466,067, filed Apr. 29, 2003, which is incorporated herein by reference.
  • The present invention further evaluates the correlation between peripheral blood gene expression and clinical outcome of solid tumors. Prognosis genes for a variety of solid tumors can be identified by the present invention. These genes are differentially expressed in peripheral blood samples of solid tumor patients who have different clinical outcomes. In many embodiments, the peripheral blood expression profiles of the prognosis genes of the present invention are correlated with patient outcome under statistical methods or correlation models. Exemplary statistical methods and correlation models include, but are not limited to, Spearman's rank correlation, Cox proportional hazard regression model, ANOVA/t test, nearest-neighbor analysis, and other rank tests, survival models or class-based correlation metrics.
  • Solid tumors amenable to the present invention include, without limitation, RCC, prostate cancer, head/neck cancer, ovarian cancer, testicular cancer, brain tumor, breast cancer, lung cancer, colon cancer, pancreas cancer, stomach cancer, bladder cancer, skin cancer, cervical cancer, uterine cancer, and liver cancer. In one embodiment, the solid tumors do not have their origin in blood or lymph (hematopoetic) cells. Solid tumors can be measured or evaluated using direct or indirect visualization procedures. Suitable visualization methods include, but are not limited to, scans (such as X-rays, computerized axial tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), or ultrasonography (U/S)), biopsy, palpation, endoscopy, laparoscopy, and other suitable means as appreciated by those skilled in the art.
  • Clinical outcome of solid tumors can be assessed by numerous criteria. In many embodiments, clinical outcome is assessed based on patients' response to a therapeutic treatment. Examples of clinical outcome measures include, without limitation, complete response, partial response, minor response, stable disease, progressive disease, time to disease progression (TTP), time to death (TTD or Survival), or any combination thereof. Examples of solid tumor treatments include, without limitation, drug therapy (e.g., CCI-779 therapy), chemotherapy, hormone therapy, radiotherapy, immunotherapy, surgery, gene therapy, anti-angiogenesis therapy, palliative therapy, or any combination thereof, or other conventional or non-conventional therapies.
  • In one embodiment, clinical outcome is evaluated based on the WHO Reporting Criteria, such as those described in WHO Publication, No. 48 (World Health Organization, Geneva, Switzerland, 1979). Under the Criteria, uni- or bidimensionally measurable lesions are measured at each assessment. When multiple lesions are present in any organ, up to 6 representative lesions can be selected, if available.
  • In another embodiment, clinical outcome is determined based on a classification system composed of clinical categories such as complete response, partial response, minor response, stable disease, progressive disease, or any combination thereof. “Complete response” (CR) means complete disappearance of all measurable and evaluable disease, determined by two observations not less than 4 weeks apart. There is no new lesion and no disease related symptom. “Partial response” (PR) in reference to bidimensionally measurable disease means decrease by at least about 50% of the sum of the products of the largest perpendicular diameters of all measurable lesions as determined by 2 observations not less than 4 weeks apart. “Partial response” in reference to unidimensionally measurable disease means decrease by at least about 50% in the sum of the largest diameters of all lesions as determined by 2 observations not less than 4 weeks apart. It is not necessary for all lesions to have regressed to qualify for partial response, but no lesion should have progressed and no new lesion should appear. The assessment should be objective. “Minor response” in reference to bidimensionally measurable disease means about 25% or greater decrease but less than about 50% decrease in the sum of the products of the largest perpendicular diameters of all measurable lesions. “Minor response” in reference to unidimensionally measurable disease means decrease by at least about 25% but less than about 50% in the sum of the largest diameters of all lesions.
  • “Stable disease” (SD) in reference to bidimensionally measurable disease means less than about 25% decrease or less than about 25% increase in the sum of the products of the largest perpendicular diameters of all measurable lesions. “Stable disease” in reference to unidimensionally measurable disease means less than about 25% decrease or less than about 25% increase in the sum of the diameters of all lesions. No new lesions should appear. “Progressive disease” (PD) refers to a greater than or equal to about a 25% increase in the size of at least one bidimensionally (product of the largest perpendicular diameters) or unidimensionally measurable lesion or appearance of a new lesion. The occurrence of pleural effusion or ascites is also considered as progressive disease if this is substantiated by positive cytology. Pathological fracture or collapse of bone is not necessarily evidence of disease progression.
  • In yet another embodiment, overall subject tumor response for uni- and bidimensionally measurable disease is determined according to Table 1.
    TABLE 1
    Overall Subject Tumor Response
    Response in Response in
    Bidimensionally Unidimensionally Overall Subject
    Measurable Disease Measurable Disease Tumor Response
    PD Any PD
    Any PD PD
    SD SD or PR SD
    SD CR PR
    PR SD or PR or CR PR
    CR SD or PR PR
    CR CR CR
  • Overall subject tumor response for non-measurable disease can be assessed, for instance, in the following situations:
    • a) Overall complete response: if non-measurable disease is present, it should disappear completely. Otherwise, the subject cannot be considered as an “overall complete responder.”
    • b) Overall progression: in case of a significant increase in the size of non-measurable disease or the appearance of a new lesion, the overall response will be progression.
  • Clinical outcome can also be assessed by other criteria. For instance, clinical outcome can be measured by TTP or TTD. TTP refers to the interval from the date of initiation of a therapeutic treatment until the first day of measurement of progressive disease. TTD refers to the interval from the date of initiation of a therapeutic treatment to the time of death, or censored at the last date known alive.
  • Moreover, clinical outcome can include prognoses based on traditional clinical risk assessment methods. In many cases, these risk assessment methods employ numerous prognostic factors to classify patients into different prognosis or risk groups. One example is Motzer risk assessment for RCC, as described in Motzer, et al., J CLIN ONCOL, 17:2530-2540 (1999). Patients in different risk groups may have different responses to a therapy.
  • Peripheral blood samples employed in the present invention can be isolated from solid tumor patients at any disease or treatment stage. In one embodiment, the peripheral blood samples are isolated from solid tumor patients prior to a therapeutic treatment. These blood samples are “baseline samples” with respect to the therapeutic treatment.
  • A variety of peripheral blood samples can be used in the present invention. In one embodiment, the peripheral blood samples are whole blood samples. In another embodiment, the peripheral blood samples comprise enriched PBMCs. By “enriched,” it means that the percentage of PBMCs in the sample is higher than that in whole blood. In some cases, the PBMC percentage in an enriched sample is at least 1, 2, 3, 4, 5 or more times higher than that in whole blood. In some other cases, the PBMC percentage in an enriched sample is at least 90%, 95%, 98%, 99%, 99.5%, or more. Blood samples containing enriched PBMCs can be prepared using any method known in the art, such as Ficoll gradients centrifugation or CPTs (cell purification tubes).
  • The relationship between peripheral blood gene expression profiles and patient outcome can be evaluated using global gene expression analyses. Methods suitable for this purpose include, but are not limited to, nucleic acid arrays (such as cDNA or oligonucleotide arrays), 2-dimensional SDS-polyacrylamide gel electrophoresis/mass spectrometry, and other high throughput nucleotide or polypeptide detection techniques.
  • Nucleic acid arrays allow for quantitative detection of the expression levels of a large number of genes at one time. Examples of nucleic acid arrays include, but are not limited to, Genechip® microarrays from Affymetrix (Santa Clara, Calif.), cDNA microarrays from Agilent Technologies (Palo Alto, Calif.), and bead arrays described in U.S. Pat. Nos. 6,288,220 and 6,391,562.
  • The polynucleotides to be hybridized to nucleic acid arrays can be labeled with one or more labeling moieties to allow for detection of hybridized polynucleotide complexes. The labeling moieties can include compositions that are detectable by spectroscopic, photochemical, biochemical, bioelectronic, immunochemical, electrical, optical or chemical means. Exemplary labeling moieties include radioisotopes, chemiluminescent compounds, labeled binding proteins, heavy metal atoms, spectroscopic markers such as fluorescent markers and dyes, magnetic labels, linked enzymes, mass spectrometry tags, spin labels, electron transfer donors and acceptors, and the like. Unlabeled polynucleotides can also be employed. The polynucleotides can be DNA, RNA, or a modified form thereof.
  • Hybridization reactions can be performed in absolute or differential hybridization formats. In the absolute hybridization format, polynucleotides derived from one sample, such as PBMCs from a patient in a selected outcome class, are hybridized to the probes on a nucleic acid array. Signals detected after the formation of hybridization complexes correlate to the polynucleotide levels in the sample. In the differential hybridization format, polynucleotides derived from two biological samples, such as one from a patient in a first outcome class and the other from a patient in a second outcome class, are labeled with different labeling moieties. A mixture of these differently labeled polynucleotides is added to a nucleic acid array. The nucleic acid array is then examined under conditions in which the emissions from the two different labels are individually detectable. In one embodiment, the fluorophores Cy3 and Cy5 (Amersham Pharmacia Biotech, Piscataway N.J.) are used as the labeling moieties for the differential hybridization format.
  • Signals gathered from nucleic acid arrays can be analyzed using commercially available software, such as those provide by Affymetrix or Agilent Technologies. Controls, such as for scan sensitivity, probe labeling and cDNA/cRNA quantitation, can be included in the hybridization experiments. In many embodiments, the nucleic acid array expression signals are scaled or normalized before being subject to further analysis. For instance, the expression signals for each gene can be normalized to take into account variations in hybridization intensities when more than one array is used under similar test conditions. Signals for individual polynucleotide complex hybridization can also be normalized using the intensities derived from internal normalization controls contained on each array. In addition, genes with relatively consistent expression levels across the samples can be used to normalize the expression levels of other genes. In one embodiment, the expression levels of the genes are normalized across the samples such that the mean is zero and the standard deviation is one. In another embodiment, the expression data detected by nucleic acid arrays are subject to a variation filter which excludes genes showing minimal or insignificant variation across all samples.
  • The gene expression data collected from nucleic acid arrays can be correlated with clinical outcome using a variety of methods. Suitable correlation methods include, but are not limited to, statistical methods (such as Spearman's rank correlation, Cox proportional hazard regression model, ANOVA/t test, or other suitable rank tests or survival models) and class-based correlation metrics (such as nearest-neighbor analysis).
  • In one aspect, class-based correlation metrics are used to identify the correlation between peripheral blood gene expression and clinical outcome. In one embodiment, patients with a specified solid tumor are divided into at least two classes based on their clinical stratifications. The correlation between peripheral blood gene expression (e.g., in PBMCs) and clinical outcome is analyzed by a supervised cluster algorithm. Exemplary supervised clustering algorithms include, but are not limited to, nearest-neighbor analysis, support vector machines, and SPLASH. Under the supervised cluster algorithms, clinical outcome of each class of patients is either known or determinable. Genes that are differentially expressed in peripheral blood cells (e.g., PBMCs) of one class of patients relative to the other class of patients can be identified. In many cases, the genes thus identified are substantially correlated with a class distinction between the two classes of patients. The genes thus identified can be used as surrogate markers for predicting clinical outcome of the solid tumor in a patient of interest.
  • In another embodiment, patients with a specified solid tumor can be divided into at least two classes based on gene expression profiles in their peripheral blood cells. Methods suitable for this purpose include unsupervised clustering algorithms, such as self-organized maps (SOMs), k-means, principal component analysis, and hierarchical clustering. A substantial number (e.g., at least 50%, 60%, 70%, 80%, 90%, or more) of patients in one class may have a first clinical outcome, and a substantial number of patients in the other class may have a second clinical outcome. Genes that are differentially expressed in the peripheral blood cells of one class of patients relative to the other class of patients can be identified. These genes are prognosis genes for the solid tumor.
  • In yet another embodiment, patients with a specified solid tumor can be divided into three or more classes based on their clinical stratifications or peripheral blood gene expression profiles. Multi-class correlation metrics can be employed to identify genes that are differentially expressed in these classes. Exemplary multi-class correlation metrics include, but are not limited to, GeneCluster 2 software provided by MIT Center for Genome Research at Whitehead Institute (Cambridge, Mass.).
  • In a further embodiment, nearest-neighbor analysis (also known as neighborhood analysis) is used to analyze gene expression data gathered from nucleic acid arrays. The algorithm for neighborhood analysis is described in Golub, et al., SCIENCE, 286: 531-537 (1999), Slonim, et al., PROCS. OF THE FOURTH ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY, Tokyo, Japan, April 8-11, p 263-272 (2000), and U.S. Pat. No. 6,647,341, all of which are incorporated herein by reference. Under one form of the neighborhood analysis, the expression profile of each gene can be represented by an expression vector g=(e1, e2, e3, . . . , en), where ei corresponds to the expression level of gene “g” in the ith sample. A class distinction can be represented by an idealized expression pattern c=(c1, c2, c3, . . . , cn), where ci=1 or −1, depending on whether the ith sample is isolated from class 0 or class 1. Class 0 may include patients having a first clinical outcome, and class 1 includes patients having a second clinical outcome. Other forms of class distinction can also be employed. Typically, a class distinction represents an idealized expression pattern, where the expression level of a gene is uniformly high for samples in one class and uniformly low for samples in the other class.
  • The correlation between gene “g” and the class distinction can be measured by a signal-to-noise score:
    P(g,c)=[μ1(g)−μ2(g)]/[σ1(g)+σ2(g)]
    where μ1(g) and μ2(g) represent the means of the log-transformed expression levels of gene “g” in class 0 and class 1, respectively, and σ1(g) and σ2(g) represent the standard deviation of the log-transformed expression levels of gene “g” in class 0 and class 1, respectively. A higher absolute value of a signal-to-noise score indicates that the gene is more highly expressed in one class than in the other. In one embodiment, the samples used to derive the signal-to-noise score comprise enriched or purified PBMCs. Thus, the signal-to-noise score P(g,c) can represent a correlation between the class distinction and the expression level of gene “g” in PBMCs.
  • The correlation between gene “g” and the class distinction can also be measured by other methods, such as by the Pearson correlation coefficient or the Euclidean distance, as appreciated by those skilled in the art.
  • The significance of the correlation between peripheral blood gene expression patterns and the class distinction can be evaluated using a random permutation test. An unusually high density of genes within the neighborhoods of the class distinction, as compared to random patterns, suggests that many genes have expression patterns that are significantly correlated with the class distinction. The correlation between genes and the class distinction can be diagrammatically viewed through a neighborhood analysis plot, in which the y-axis represents the number of genes within various neighborhoods around the class distinction and the x-axis indicates the size of the neighborhood (i.e., P(g,c)). Curves showing different significance levels for the number of genes within corresponding neighborhoods of randomly permuted class distinctions can also be included in the plot.
  • In one embodiment, the prognosis genes of the present invention are substantially correlated with a class distinction between two outcome classes. In one example, the prognosis genes are above the median significance level in the neighborhood analysis plot. This means that the correlation measure P(g,c) for each prognosis gene is such that the number of genes within the neighborhood of the class distinction having the size of P(g,c) is greater than the number of genes within the corresponding neighborhoods of randomly permuted class distinctions at the median significance level. In another example, the employed prognosis genes are above the 10%, 5%, 2%, or 1% significance level. As used herein, x % significance level means that x % of random neighborhoods contain as many genes as the real neighborhood around the class distinction.
  • Class predictors can be constructed using the prognosis genes of the present invention. These class predictors are useful for assigning class membership to solid tumor patients. In one embodiment, the prognosis genes in a class predictor are limited to those shown to be significantly correlated with the class distinction by the permutation test, such as those at above the 1%, 2%, 5%, 10%, 20%, 30%, 40%, or 50% significance level. In another embodiment, the expression level of each prognosis gene in a class predictor is substantially higher or substantially lower in PBMCs of one class of patients than in the other class of patients. In still another embodiment, the prognosis genes in a class predictor have top absolute values of P(g,c). In yet another embodiment, the p-value under a Student's t-test (e.g., two-tailed distribution, two sample unequal variance) for each differentially expressed prognosis gene is no more than 0.05, 0.01, 0.005, 0.001, 0.0005, 0.0001, or less.
  • In a further embodiment, the class predictors of the present invention have at least 50% accuracy for leave-one-out cross validation. In another embodiment, the class predictors of the present invention have at least 60%, 70%, 80%, 90%, 95%, or 99% accuracy for leave-one-out cross validation.
  • In another aspect, the correlation between peripheral blood gene expression profiles and clinical outcome can be evaluated by statistical methods. Clinical outcome suitable for these analyses includes, but are not limited to, TTP, TTD, and other time-associated clinical indicators. One exemplary statistical method employs Spearman's rank correlation coefficient, which has the formula of:
    r s =SS UV/(SS UU SS VV)1/2
    where SSUV=ΣUiVi−[(ΣUi)(ΣVi)]/n, SSUU=ΣVi 2−[(ΣVi)2]/n, and SSVV=ΣUi 2−[ΣUi)2]/n. Ui is the expression level ranking of a gene of interest, Vi is the ranking of the clinical outcome, and n represents the number of patients. The shortcut formula for Spearman's rank correlation coefficient is rs=1−(6×Σdi 2)/[n(n2−1)], where di=Ui−Vi. The Spearman's rank correlation is similar to the Pearson's correlation except that it is based on ranks and is thus more suitable for data that is not normally distributed. See, for example, Snedecor and Cochran, STATISTICAL METHODS, Eight edition, Iowa State University Press, Ames, Iowa, 503 pp, 1989. The correlation coefficient is tested to assess whether it differs significantly from a value of 0 (i.e., no correlation).
  • The correlation coefficients for each prognosis gene identified by the Spearman's rank correlation can be either positive or negative, provided that the correlation is statistically significant. In many embodiments, the p-value for each prognosis gene thus identified is no more than 0.05, 0.01, 0.005, 0.001, 0.0005, 0.0001, or less. In many other embodiments, the Spearman correlation coefficients of the prognosis genes thus identified have absolute values of at least 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or more.
  • Another exemplary statistical method is Cox proportional hazard regression model, which has the formula of:
    log h i(t)=α(t)+βj x ij
    where hi(t) is the hazard function that assesses the instantaneous risk of demise at time t, conditional on survival to that time, α(t) is the baseline hazard function, and xij is a covariate which may represent, for example, the expression level of prognosis gene j in a peripheral blood sample. See Cox, JOURNAL OF THE ROYAL STATISTICAL SOCIETY, SERIES B 34:187 (1972). Additional covariates, such as interactions between covariates, can also be included in Cox proportional hazard model. As used herein, the terms “demise” or “survival” are not limited to real death or survival. Instead, these terms should be interpreted broadly to cover any type of time-associated events, such as TTP. In many cases, the p-values for the correlation under Cox proportional hazard regression model are no more than 0.05, 0.01, 0.005, 0.001, 0.0005, 0.0001, or less. The p-values for the prognosis genes identified under Cox proportional hazard regression model can be determined by the likelihood ratio test, Wald test, the Score test, or the log-rank test. In one embodiment, the hazard ratios for the prognosis genes thus identified are at least 1.5, 2, 3, 4, 5, or more. In another embodiment, the hazard ratios for the prognosis genes thus identified are no more than 0.67, 0.5., 0.33, 0.25., 0.2, or less.
  • Other rank tests, scores, measurements, or models can also be employed to identify prognosis genes whose expression profiles in peripheral blood samples are correlated with clinical outcome of solid tumors. These tests, scores, measurements, or models can be either parametric or nonparametric, and the regression may be either linear or non-linear. Many statistical methods and correlation/regression models can be carried out using commercially available programs.
  • Other methods capable of identifying genes differentially expressed in peripheral blood cells of one class of patients relative to another class of patients can be used. These methods include, but are not limited, RT-PCR, Northern Blot, in situ hybridization, and immunoassays such as ELISA, RIA or Western Blot. The expression levels of genes thus identified can be substantially higher or substantially lower in peripheral blood cells (e.g., PBMCs) of one class of patients than in another class of patients. In some cases, the average peripheral blood expression level of a prognosis gene in PBMCs of one class of patients can be at least 2, 3, 4, 5, 10, 20, or more folds higher or lower than that in another class of patients. In many embodiments, the p-value of an appropriate statistical significance test (e.g., Student's t-test) for the difference between average expression levels is no more than 0.05, 0.01, 0.005, 0.001, 0.0005, 0.0001, or less.
  • Prognosis genes for other non-blood diseases can be similarly identified according to the present invention, provided that the correlation between peripheral blood gene expression and clinical outcome of these diseases, is statistically significant. The peripheral blood expression patterns of the prognosis genes thus identified are indicative of clinical outcome of these diseases.
  • II. Identification of RCC Prognosis Genes
  • RCC comprises the majority of all cases of kidney cancer and is one of the ten most common cancers in industrialized countries, comprising 2% of adult malignancies and 2% of cancer-related deaths. Several prognostic factors and scoring indices have been developed for patients diagnosed with RCC, typified by multivariate assessments of several key indicators. As an example, one prognostic scoring system employs the five prognostic factors proposed by Motzer, et al., supra—namely, Karnofsky performance status, serum lactate dehydrognease, hemoglobin, serum calcium, and presence/absence of prior nephrectomy.
  • The present invention identifies numerous RCC prognosis genes whose peripheral blood expression profiles correlate with patient outcome in CCI-779 therapy. In a clinical trial, the cytostatic mTOR inhibitor CCI-779 was evaluated in RCC patients for its anti-cancer effect. PBMCs collected prior to CCI-779 therapy were analyzed on oligonucleotide arrays in order to determine whether mononuclear cells from RCC patients possessed transcriptional patterns predictive of patient outcome. The results of both supervised and unsupervised analyses indicated that transcriptional profiles in the surrogate tissue of PBMCs from RCC patients prior to treatment with CCI-779 are significantly correlated with patient outcome.
  • PBMCs were isolated prior to CCI-779 therapy from peripheral blood of 45 advanced RCC patients (18 females and 27 males) participating in a phase 2 clinical trial study. Written informed consent for the pharmacogenomic portion of the clinical study was received for all individuals and the project was approved by the local Institutional Review Boards at the participating clinical sites. RCC tumors of patients were classified at the clinical sites as conventional (clear cell) carcinomas (24), granular (1), papillary (3), or mixed subtypes (7). Ten tumors were classified as unknown. RCC patients were primarily of Caucasian descent (44 Caucasian, 1 African-American) and had a mean age of 58 years (range of 40-78 years). Inclusion criteria included patients with histologically confirmed advanced renal cancer who had received prior therapy for advanced disease, or who had not received prior therapy for advanced disease but were not appropriate candidates to receive high doses of IL-2 therapy. Other inclusion criteria included patients with (1) bi-dimensionally measurable evidence of disease; (2) evidence of progression of the disease prior to study entry; (3) an age of 18 years or older; (4) ANC>1500/μL, platelet>100,000/μL and hemoglobin>8.5 g/dL; (5) adequate renal function evidenced by serum creatinine<1.5× upper limit of normal; (6) adequate hepatic function evidenced by biliruubin<1.5× upper limit of normal and AST<3× upper limit of normal (or AST<5× upper limit of normal if liver metastases were present); (7) serum cholesterol<350 mg/dL, triglycerides<300 mg/dL; (8) ECOG performance status 0-1; and (9) a life expectancy of at least 12 weeks. Exclusion criteria included patients who had (1) the presence of known CNS metastases; (2) surgery or radiotherapy within 3 weeks of start of dosing; (3) chemotherapy or biologic therapy for RCC within 4 weeks of start of dosing; (4) treatment with a prior investigational agent within 4 weeks of start of dosing; (5) immunocompromised status including those known to be HIV positive, or receiving concurrent use of immunosuppressive agents including corticosteroids; (6) active infections; (7) required treatment with anticonvulsant therapy; (8) presence of unstable angina/myocardial infarction within 6 months/ongoing treatment of life-threatening arrythmia; (9) history of prior malignancy in past 3 years; (10) hypersensitivity to macrolide antibiotics; and (11) pregnancy or any other illness which would substantially increase the risk associated with participation in the study.
  • These advanced RCC patients were treated with one of 3 doses of CCI-779 (25 mg, 75 mg, or 250 mg) administered as a 30 minute intravenous (IV) infusion once weekly for the duration of the trial. CCI-779 is an ester analog of the immunosuppressant rapamycin and as such is a potent, selective inhibitor of the mammalian target of rapamycin. The mammalian target of rapamycin (mTOR) activates multiple signaling pathways, including phosphorylation of p70s6kinase, which results in increased translation of 5′ TOP mRNAs encoding proteins involved in translation and entry into the G1 phase of the cell cycle. By virtue of its inhibitory effects on mTOR and cell cycle control, CCI-779 functions as a cytostatic and immunosuppressive agent.
  • Clinical staging and size of residual, recurrent or metastatic disease were recorded prior to treatment and every 8 weeks following initiation of CCI-779 therapy. Tumor size was measured in centimeters and reported as the product of the longest diameter and its perpendicular. Measurable disease was defined as any bidimensionally measurable lesion where both diameters>1.0 cm by CT-scan, X-ray or palpation. Tumor response was determined by the sum of the products of all measurable lesions. The categories for assignment of clinical response were given by the clinical protocol definitions (i.e., progressive disease, stable disease, minor response, partial response, and complete response). The category for assignment of prognosis under the Motzer risk assessment (favorable vs intermediate vs poor) was also used. Among the 45 RCC patients, 6 were assigned a favorable risk assessment, 17 patients possessed an intermediate risk score, and 22 patients received a poor prognosis classification. In addition to the categorical classifications, overall survival and time to disease progression were also monitored as clinical endpoints.
  • HgU95A genechips (manufactured by Affymetrix) were used to detect baseline expression profiles in PBMCs of the RCC patients prior to the CCI-779 therapy. Each HgU95A genechip comprises over 12,600 human sequences according to the Affymetrix Expression Analysis Technical Manual. RNA transcripts were first isolated from PBMCs of the RCC patients. cRNA was then prepared and hybridized to the genechips according to protocols described in the Affymetrix's Expression Analysis Technical Manual. Hybridization signals were collected, scaled, and normalized before being subject to further analysis. In one example, the log of the expression level for each gene was normalized across the samples such that the mean is zero and the standard deviation is one.
  • The expression profiling analysis revealed that of the 12,626 genes on the HgU95A chip, 5,424 genes met the initial criteria (i.e., at least 1 present call across the data set and at least 1 frequency≧10 ppm). On average, 4,023 transcripts were detected as “present” in any given RCC PBMC profile.
  • In an initial assessment of the expression data in baseline PBMCs, pairwise correlations were calculated to assess the association between gene expression levels measured by HgU95A Affymetrix microarrays and continuous measures of clinical outcome. Correlations were run using expression levels from each of 5,424 qualifiers that passed the initial criteria. Correlations were run for two clinical measures (TTD and TTP) and for one measure of baseline expression level (log2-transformed scaled frequency in units of ppm).
  • In one example, Spearman's rank correlations were computed. The p-value for the hypothesis that the correlation was equal to 0 was calculated for each pairwise correlation. For each comparison between clinical outcome and gene expression, the number of tests that were nominally significant out of the 5,424 tests performed was calculated for five Type I (i.e. false-positive) error levels. To adjust for the fact that 5,424 non-independent tests were performed, a permutation-based approach was employed to evaluate how often the observed number of significance tests would be found under the null hypothesis of no correlation.
  • The overall results for Spearman's rank correlation comparisons of clinical outcome with baseline expression levels (log2-transformed scaled frequency) are summarized in Tables 2a and 2b. Each table shows alpha confidence levels (“α”), the observed numbers of transcripts that have nominally significant Spearman correlations with the clinical outcome of interest (“Observed Number”), and the percentage of permutations for which number of nominally significant Spearman correlations equals or exceeds the number observed (“%-age of Permutations”). Evidence for association between clinical outcome and baseline gene expression in PBMCs was significant for both TTD and TTP.
    TABLE 2a
    Spearman Correlations of Clinical Outcome with Baseline
    Expression Levels in PBMCs of RCC Patients in CCI-779
    Therapy (n = 45 patients)
    Time to Disease Progression
    Observed Number of
    Nominally %-age of Permutations for
    Significant which Number of Nominally Significant
    Spearman Spearman Correlations
    α Correlations* equals or exceeds observed number
    0.1 1127 5.3% (53/1000)
    0.05 749 3.8% (38/1000)
    0.01 248 3.1% (31/1000)
    0.005 159 2.6% (26/1000)
    0.001 51 2.5% (25/1000)

    *based on 5,424 genes (filtered by at least one Present and at least one frequency ≧ 10 ppm)
  • TABLE 2b
    Spearman Correlations of Clinical Outcome with Baseline
    Expression Levels in PBMCs of RCC Patients in CCI-779
    Therapy (n = 45 patients)
    Time to Death
    %-age of Permutations
    Observed Number of for which Number of Nominally
    Nominally Significant Spearman Correlations
    Significant Spearman equals or exceeds observed
    α Correlations* number
    0.1 1604 0.1% (1/1000)
    0.05 1117 0.1% (1/1000)
    0.01 436 0.1% (1/1000)
    0.005 289 0.1% (1/1000)
    0.001 105 0.3% (3/1000)

    *based on 5,424 genes (filtered by at least one Present and at least one frequency ≧ 10 ppm)
  • Table 3 lists the results of the Spearman's rank correlation analyses for all of the 5,424 genes that met the initial criteria. Each gene has a corresponding qualifier on the HgU95A genechip, and each qualifier represents multiple oligonucleotide probes that are stably attached to discrete regions on the HgU95A genechip. According to the design, RNA transcripts of a gene, or the complements thereof, are expected to hybridize under nucleic acid array hybridization conditions to the corresponding qualifier on the HgU95A genechip. As used herein, a polynucleotide can hybridize to a qualifier if the polynucleotide, or the complement thereof, can hybridize to at least one oligonucleotide probe of the qualifier. In many embodiments, the polynucleotide or the complement thereof can hybridize to at least 50%, 60%, 70%, 80%, 90% or 100% of all of the oligonucleotide probes of the qualifier.
  • Each gene or qualifier in Table 3 may have a corresponding SEQ ID NO or Entrez accession number from which the oligonucleotide probes of the qualifier can be derived. In many instances, a polypeptide capable of hybridizing to a qualifier can also hybridize to the sequence of the corresponding SEQ ID NO or Entrez accession number, or the complement thereof. The sequence of each Entrez accession number can be obtained from the Entrez nucleotide database at the National Center of Biotechnology Information (NCBI). The Entrez nucleotide database collects sequences from several sources, including GenBank, RefSeq, and PDB. Each SEQ ID NO may be derived from the sequence of the corresponding Entrez accession number. Table 4 shows the Entrez and Unigene accession numbers for all of the qualifiers on the HgU95A genechip that met the initial criteria.
  • Any ambiguous residue (“n”) in a SEQ ID NO can be determined by a variety of methods. In one embodiment, the ambiguous residues in a SEQ ID NO are determined by aligning the SEQ ID NO to a corresponding genomic sequence obtained from a human genome sequence database. In another embodiment, the ambiguous residues in a SEQ ID NO are determined based on the sequence of the corresponding Entrez accession number. In yet another embodiment, the ambiguous residues are determined by re-sequencing the SEQ ID NO.
  • Genes associated with each qualifier on the HgU95A genechip can be identified based on the annotations provided by Affymetrix. All of the genes thus identified are listed in Tables 3 and 5. These genes can also be identified based on their corresponding Entrez or Unigene accession numbers. In addition, these genes can be determined by BLAST searching their corresponding SEQ ID NOs, or the unambiguous segments thereof, against a human genome sequence database. Suitable human genome sequence databases for this purpose include, but are not limited to, the NCBI human genome database. The NCBI provides BLAST programs, such as “blastn,” for searching its sequence databases.
  • In one embodiment, the BLAST search of the NCBI human genome database is carried out by using an unambiguous segment (e.g., the longest unambiguous segment) of a SEQ ID NO. Gene(s) that aligns to the unambiguous segment with significant sequence identity can be identified. In many cases, the identified gene(s) has at least 95%, 96%, 97%, 98%, 99%, or more sequence identity with the unambiguous segment.
  • On the basis of Spearman's rank correlation, prognosis genes that are highly correlated with TTP or TTD were identified. Table 6a lists examples of genes whose expression levels are positively correlated with TTP. Table 6b depicts examples of genes whose expression levels are negatively correlated with TTP. Table 6c provides examples of genes whose expression levels are positively correlated with TTD. Table 6d shows examples of genes whose expression levels are negatively correlated with TTD. Correlation coefficients, p-values, and the corresponding qualifiers are also indicated for each gene in Tables 6a, 6b, 6c, and 6d.
    TABLE 6a
    Prognosis Genes Positively Correlated with TTP
    HgU95A Correlation P-
    SEQ ID NO: Qualifier Coefficient Value Gene Name
    757 38518_at 0.6019 0.0000 SCML2
    1835 37343_at 0.5932 0.0000 ITPR3
    318 41174_at 0.5925 0.0000 RANBP2L1
    755 41669_at 0.5908 0.0000 KIAA0191
    1619 40584_at 0.5602 0.0001 NUP88
    1734 41767_r_at 0.5591 0.0001 KIAA0855
    158 38256_s_at 0.5551 0.0001 DKFZP564O092
    1122 39829_at 0.5508 0.0001 ARL7
    1275 35802_at 0.5475 0.0001 KIAA1014
    452 32169_at 0.5407 0.0001 KIAA0875
    263 41562_at 0.5272 0.0002 BMI1
    39 35753_at 0.5226 0.0002 PRP8
    238 40905_s_at 0.5223 0.0002 DKFZP566J153
    373 41547_at 0.5189 0.0003 BUB3
    1372 37416_at 0.5177 0.0003 ARHH
    237 37585_at 0.5157 0.0003 SNRPA1
    483 34716_at 0.5143 0.0003 TASR
    603 32183_at 0.5034 0.0004 SFRS11
    768 39426_at 0.4977 0.0005 CA150
    1633 35815_at 0.4975 0.0005 HYPB
    1253 36403_s_at 0.4972 0.0005 UNK_AI434146
    225 40828_at 0.4963 0.0005 P85SPR
    1119 35364_at 0.4947 0.0006 APPBP1
    423 33861_at 0.4931 0.0006 UNK_AI123426
    231 36474_at 0.4927 0.0006 KIAA0776
    346 35764_at 0.4908 0.0006 CXORF5
    840 39129_at 0.4904 0.0006 UNK_AF052134
    248 32508_at 0.4893 0.0006 KIAA1096
    935 35842_at 0.4862 0.0007 UNK_AL049265
    278 41737_at 0.4862 0.0007 SRM160
    120 36303_f_at 0.4833 0.0008 ZNF85
    223 34256_at 0.4829 0.0008 SIAT9
    79 33845_at 0.4828 0.0008 HNRPH1
    808 40048_at 0.4822 0.0008 UNK_D43951
    77 37625_at 0.4801 0.0008 IRF4
    535 33234_at 0.4779 0.0009 UNK_AA887480
    1689 2000_at 0.4777 0.0009 ATM
    820 37078_at 0.4760 0.0010 CD3Z
    427 38778_at 0.4744 0.0010 KIAA1046
  • TABLE 6b
    Prognosis Genes Negatively Correlated with TTP
    HgU95A Correlation P-
    SEQ ID NO: Qualifier Coefficient Value Gene Name
    5299 935_at −0.6319 0.0000 CAP
    4559 34498_at −0.5385 0.0001 VNN2
    5296 37023_at −0.5292 0.0002 LCP1
    5303 286_at −0.5189 0.0003 H2AFO
    5200 38831_f_at −0.5152 0.0003 UNK_AF053356
    4988 268_at −0.5126 0.0003 PECAM1
    5059 38893_at −0.5006 0.0005 NCF4
    4509 34319_at −0.4950 0.0005 S100P
    4899 37328_at −0.4931 0.0006 PLEK
    4664 181_g_at −0.4925 0.0006 UNK_S82470
    4939 38894_g_at −0.4852 0.0007 NCF4
    5208 32736_at −0.4805 0.0008 UNK_W68830
  • TABLE 6c
    Prognosis Genes Positively Correlated with TTD
    HgU95A Correlation P-
    SEQ ID NO: Qualifier Coefficient Value Gene Name
    16 37385_at 0.6524 0.0000 CYP
    1 41606_at 0.6155 0.0000 DRG1
    271 33420_g_at 0.6043 0.0000 API5
    5 35353_at 0.5969 0.0000 PSMC2
    614 38017_at 0.5942 0.0000 CD79A
    213 31851_at 0.5854 0.0000 RFP2
    27 35319_at 0.5817 0.0000 CTCF
    11 38702_at 0.5702 0.0000 UNK_AF070640
    231 36474_at 0.5654 0.0001 KIAA0776
    223 34256_at 0.5649 0.0001 SIAT9
    201 34763_at 0.5575 0.0001 CSPG6
    129 33831_at 0.5561 0.0001 CREBBP
    33 229_at 0.5499 0.0001 CBF2
    43 37381_g_at 0.5478 0.0001 GTF2B
    1261 40092_at 0.5436 0.0001 BAZ2A
    145 39746_at 0.5428 0.0001 POLR2B
    318 41174_at 0.5424 0.0001 RANBP2L1
    248 32508_at 0.5397 0.0001 KIAA1096
    90 33403_at 0.5390 0.0001 DKFZP547E1010
    110 39809_at 0.5381 0.0001 HBP1
    303 34829_at 0.5373 0.0001 DKC1
    77 37625_at 0.5350 0.0002 IRF4
    38 35656_at 0.5336 0.0002 RNF6
    450 39509_at 0.5328 0.0002 UNK_AI692348
    53 33543_s_at 0.5324 0.0002 PNN
    398 38082_at 0.5318 0.0002 KIAA0650
    120 36303_f_at 0.5311 0.0002 ZNF85
    154 1885_at 0.5300 0.0002 ERCC3
    284 32194_at 0.5285 0.0002 CBF2
    605 41621_i_at 0.5264 0.0002 ZNF266
    76 33151_s_at 0.5239 0.0002 UNK_W25932
    452 32169_at 0.5212 0.0002 KIAA0875
    32 36845_at 0.5203 0.0002 KIAA0136
    771 36231_at 0.5197 0.0003 UNK_AC002073
    85 35163_at 0.5172 0.0003 KIAA1041
    238 40905_s_at 0.5170 0.0003 DKFZP566J153
    202 39431_at 0.5164 0.0003 NPEPPS
    755 41669_at 0.5160 0.0003 KIAA0191
    61 35294_at 0.5150 0.0003 SSA2
    1195 39401_at 0.5139 0.0003 UNK_W28264
    483 34716_at 0.5137 0.0003 TASR
    82 40563_at 0.5136 0.0003 DKFZP564A043
    255 38667_at 0.5124 0.0003 UNK_AA189161
    197 38122_at 0.5107 0.0003 SLC23A1
    237 37585_at 0.5096 0.0004 SNRPA1
    603 32183_at 0.5079 0.0004 SFRS11
    114 40816_at 0.5074 0.0004 PWP1
    13 33818_at 0.5055 0.0004 UNK_AC004472
    193 37703_at 0.5042 0.0004 RABGGTB
    2 38016_at 0.5039 0.0004 HNRPD
    56 37737_at 0.4997 0.0005 PCMT1
    24 36872_at 0.4976 0.0005 ARPP-19
    12 39415_at 0.4975 0.0005 HNRPK
    7 40252_g_at 0.4970 0.0005 HRB2
    48 39727_at 0.4966 0.0005 DUSP11
    6 1728_at 0.4966 0.0005 BMI1
    296 34967_at 0.4956 0.0005 UNK_AF001549
    69 39864_at 0.4949 0.0005 CIRBP
    22 32758_g_at 0.4947 0.0006 RAE1
    39 35753_at 0.4943 0.0006 PRP8
    188 1857_at 0.4916 0.0006 MADH7
    346 35764_at 0.4915 0.0006 CXORF5
    1045 32372_at 0.4911 0.0006 CTSB
    17 33485_at 0.4892 0.0006 RPL4
    10 34647_at 0.4887 0.0007 DDX5
    468 1442_at 0.4886 0.0007 ESR2
    97 41506_at 0.4875 0.0007 MAPKAPK5
    118 34879_at 0.4873 0.0007 DPM1
    1795 39512_s_at 0.4869 0.0007 UNK_AA457029
    66 36783_f_at 0.4865 0.0007 H-PLK
    485 35479_at 0.4860 0.0007 ADAM28
    151 40308_at 0.4858 0.0007 UNK_AI830496
    442 38462_at 0.4852 0.0007 NDUFA5
    347 781_at 0.4851 0.0007 RABGGTB
    60 38102_at 0.4850 0.0007 UNK_W28575
    158 38256_s_at 0.4829 0.0008 DKFZP564O092
    332 32850_at 0.4817 0.0008 NUP153
    94 35286_r_at 0.4815 0.0008 RY1
    49 36456_at 0.4815 0.0008 DKFZP564I052
    362 38924_s_at 0.4813 0.0008 SSH3BP1
    190 35805_at 0.4809 0.0008 DKFZP434D156
    195 40086_at 0.4805 0.0008 KIAA0261
    847 34274_at 0.4801 0.0008 KIAA1116
    322 39897_at 0.4793 0.0009 DDX16
    405 41665_at 0.4792 0.0009 KIAA0824
    52 38114_at 0.4785 0.0009 RAD21
    1490 41166_at 0.4782 0.0009 IGHM
    182 41569_at 0.4781 0.0009 KIAA0974
    517 33440_at 0.4774 0.0009 TCF8
    582 36459_at 0.4767 0.0009 KIAA0879
    414 216_at 0.4765 0.0009 PTGDS
    389 41199_s_at 0.4760 0.0009 SFPQ
    1694 40051_at 0.4756 0.0010 KIAA0057
    578 38019_at 0.4754 0.0010 CSNK1E
    565 36690_at 0.4746 0.0010 NR3C1
    373 41547_at 0.4742 0.0010 BUB3
    269 38105_at 0.4734 0.0010 UNK_W26521
    225 40828_at 0.4732 0.0010 P85SPR
    509 41809_at 0.4729 0.0010 UNK_AI656421
    8 36210_g_at 0.4727 0.0010 FSRG1
  • TABLE 6d
    Prognosis Genes Negatively Correlated with TTD
    HgU95A Correlation
    SEQ ID NO: Qualifier Coefficient P-Value Gene Name
    5303 286_at −0.5871 0.0000 H2AFO
    5279 32609_at −0.5841 0.0000 H2AFO
    5312 38483_at −0.5464 0.0001 HSA011916
    5281 769_s_at −0.5036 0.0004 ANXA2
    5286 1131_at −0.4876 0.0007 MAP2K2
    5024 32378_at −0.4818 0.0008 PKM2
    956_at −0.4770 0.0009 TUBB
    5185 37311_at −0.4760 0.0010 TALDO1
    5220 37148_at −0.4744 0.0010 LILRB3
    5272 36199_at −0.4725 0.0010 DAP
  • In addition to the specific genes described herein, the present invention contemplates the use of any other gene that can hybridize under stringent or nucleic acid array hybridization conditions to a qualifier identified in the present invention. These genes may include hypothetical or putative genes that are supported by EST or mRNA data. The expression profiles of these genes may correlate with patient clinical outcome. As used herein, a gene can hybridize to a qualifier if an RNA transcript of the gene can hybridize to at least one oligonucleotide probe of the qualifier. In many cases, an RNA transcript of the gene can hybridize to at least 50%, 60%, 70%, 80%, 90%, or more oligonucleotide probes of the qualifier.
  • The oligonucleotide probe sequences of each qualifier on HgU95A genechips may be obtained from Affymetrix or from the sequence files maintained at Affymetrix website “www.affymetrix.com/support/technical/byproduct.affx?product=hgu95sequence.” For instance, the oligonucleotide probe sequences can be found in the sequence file “HG_U95A Probe Sequences, FASTA” at the website. This sequence file is incorporated herein by reference in its entirety.
  • In another example, a Cox proportional hazard regression model was employed to assess the correlation between baseline PBMC gene expression levels and clinical outcome. Cox model can take into account the effects of censoring on correlations of gene expression with TTD (or Survival as of last known date alive) and TTP (or progression-free status as of last known date alive). Of the 45 RCC patients with baseline PBMC expression levels, 4 had censored data for TTP and 15 had censored data for TTD. Similar to the Spearman's assessment of the data, Cox regression can identify genes significantly correlated with survival and disease progression for any given α-confidence level. A similar permutation strategy can be used to affirm any correlation between baseline expression profiles and clinical outcome.
  • In one embodiment, models were fit using expression levels from each of the 5,424 qualifiers that passed the initial filtering criteria in the 45 baseline samples. TTP and TTD were tested for their association with log2-transformed scaled frequency at baseline. A SAS program was used to generate the estimates in Tables 7a and 7b. Tables 7a and 7b demonstrate a strong correlation between TTP/TTD and baseline gene expression.
    TABLE 7a
    Cox Regressions of Clinical Outcome on Baseline Expression
    Levels in PBMCs of RCC Patients in CCI-779 Therapy
    (n = 45 patients)
    Time to Progression
    Percentage of Permutations for
    which Number of Nominally
    Observed Number of Significant Cox Regressions
    Nominally Significant Equals or Exceeds Observed
    ∀ Cox Regressions* Number**
    0.1 1439 0.8% (4/500)
    0.05 950 0.8% (3/500)
    0.01 342 0.8% (4/500)
    0.005 217 0.8% (4/500)
    0.001 53 1.0% (5/500)

    *for 5,424 genes (filtered by at least one Present call and at least one frequency ≧ 10 ppm)

    **based on 500 random permutations
  • TABLE 7b
    Cox Regressions of Clinical Outcome on Baseline Expression
    Levels in PBMCs of RCC Patients in CCI-779 Therapy
    (n = 45 patients)
    Time to Death
    Percentage of Permutations for
    which Number of Nominally
    Observed Number of Significant Cox Regressions
    Nominally Significant Equals or Exceeds Observed
    ∀ Cox Regressions* Number**
    0.1 1948 <0.2% (0/500)
    0.05 1383 <0.2% (0/500)
    0.01 602 <0.2% (0/500)
    0.005 404 <0.2% (0/500)
    0.001 142 <0.2% (0/500)

    *for 5,424 genes (filtered by at least one Present call and at least one frequency ≧ 10 ppm)

    **based on 500 random permutations
  • Table 8 lists the results of Cox proportional hazard modeling for all of the 5,424 genes that met the initial criteria. Hazard ratios and p-values (for the hypothesis that the risk coefficient was equal to 1, i.e., no risk) are indicated for each gene. Examples of genes that are indicative of high risk for TTP or TTD are shown in Tables 9a or 9c, respectively. These genes have hazard ratios of at least 3. Examples of genes that are indicative of low risk for TTP or TTD are described in Tables 9b or 9d, respectively. These genes have hazard ratios of no more than 0.333.
    TABLE 9a
    Prognosis Genes Indicative of High Risk for TTP
    Hazard
    SEQ ID NO: HgU95A Qualifier Ratio P-Value Gene Name
    5296 37023_at 6.1066 0.0001 LCP1
    5299 935_at 5.8829 0.0000 CAP
    5315 40771_at 4.9503 0.0586 MSN
    5313 37298_at 4.6595 0.0046 GABARAP
    5235 31820_at 4.2099 0.0061 HCLS1
    5248 676_g_at 4.1051 0.0016 IFITM1
    4920 33906_at 3.9750 0.0106 SSSCA1
    5208 32736_at 3.8093 0.0013 UNK_W68830
    4958 40169_at 3.5692 0.0243 TIP47
    5314 39811_at 3.4197 0.1074 UNK_AA402538
    5275 1309_at 3.3680 0.0053 PSMB3
    4524 39814_s_at 3.2703 0.0029 UNK_AI052724
    5153 38605_at 3.1625 0.0592 NDUFB1
    5200 38831_f_at 3.0853 0.0092 UNK_AF053356
  • TABLE 9b
    Prognosis Genes Indicative of Low Risk for TTP
    Hazard
    SEQ ID NO: HgU95A Qualifier Ratio P-Value Gene Name
    12 39415_at 0.0818 0.0002 HNRPK
    39 35753_at 0.1608 0.0001 PRP8
    282 33667_at 0.1650 0.0890 PPIA
    79 33845_at 0.1657 0.0024 HNRPH1
    26 36186_at 0.1661 0.0040 RNPS1
    241 1420_s_at 0.1662 0.0009 EIF4A2
    127 31950_at 0.1724 0.0071 PABPC1
    10 34647_at 0.1831 0.0010 DDX5
    459 36515_at 0.2094 0.0002 GNE
    230 36111_s_at 0.2147 0.0031 SFRS2
    1287 39180_at 0.2154 0.0009 FUS
    22 32758_g_at 0.2186 0.0010 RAE1
    15 31952_at 0.2211 0.0076 RPL6
    81 38527_at 0.2258 0.0016 NONO
    232 32831_at 0.2298 0.0006 TIM17
    19 37609_at 0.2321 0.0016 NUBP1
    18 34695_at 0.2330 0.0035 GA17
    157 39730_at 0.2331 0.0005 ABL1
    689 35808_at 0.2385 0.0037 SFRS6
    246 32751_at 0.2386 0.0013 UNK_AF007140
    278 41737_at 0.2393 0.0023 SRM160
    338 32205_at 0.2431 0.0009 PRKRA
    7 40252_g_at 0.2473 0.0033 HRB2
    54 35325_at 0.2540 0.0030 UNK_AF052113
    1823 41292_at 0.2549 0.0014 HNRPH1
    2174 32658_at 0.2553 0.0010 UNK_AL031228
    242 33307_at 0.2569 0.0008 UNK_AL022316
    35 40426_at 0.2587 0.0306 BCL7B
    263 41562_at 0.2595 0.0010 BMI1
    9 34315_at 0.2638 0.0149 AFG3L2
    5046 33920_at 0.2665 0.0549 DIAPH1
    105 33706_at 0.2698 0.0114 SART1
    3048 35170_at 0.2706 0.0053 MAN2C1
    33 229_at 0.2715 0.0064 CBF2
    17 33485_at 0.2724 0.0169 RPL4
    6 1728_at 0.2736 0.0103 BMI1
    269 38105_at 0.2748 0.0017 UNK_W26521
    58 1361_at 0.2801 0.0059 TERF1
    528 32171_at 0.2831 0.0040 EIF5
    49 36456_at 0.2834 0.0015 DKFZP564I052
    2420 838_s_at 0.2841 0.0616 UBE2I
    1527 1706_at 0.2852 0.0144 ARAF1
    427 38778_at 0.2882 0.0012 KIAA1046
    93 39378_at 0.2896 0.1463 BECN1
    162 34225_at 0.2911 0.0126 UNK_AF101434
    1029 32833_at 0.2918 0.0016 CLK1
    898 34285_at 0.2938 0.0021 KIAA0795
    205 35743_at 0.2968 0.0133 NAR
    1735 39165_at 0.2971 0.0086 NIFU
    361 36685_at 0.2979 0.0045 AMD1
    285 37557_at 0.2985 0.0038 SLC4A2
    120 36303_f_at 0.2987 0.0018 ZNF85
    3896 33392_at 0.3019 0.0030 DKFZP434J154
    335 40160_at 0.3031 0.0038 DKFZP586P2220
    606 34337_s_at 0.3047 0.0009 M96
    585 37506_at 0.3053 0.0006 UNK_Z78308
    158 38256_s_at 0.3053 0.0002 DKFZP564O092
    324 37690_at 0.3053 0.0120 ILVBL
    59 1020_s_at 0.3060 0.0069 SIP2-28
    1606 36862_at 0.3066 0.0147 KIAA1115
    176 39141_at 0.3069 0.0074 ABCF1
    167 32592_at 0.3071 0.0280 KIAA0323
    340 39044_s_at 0.3076 0.0141 DGKD
    133 40596_at 0.3076 0.0058 TCOF1
    1186 34369_at 0.3078 0.0454 KIAA0214
    1189 33188_at 0.3090 0.0006 PPIL2
    1536 41220_at 0.3110 0.0404 MSF
    844 38445_at 0.3125 0.0057 ARHGEF1
    66 36783_f_at 0.3125 0.0064 H-PLK
    166 37717_at 0.3126 0.0130 NAGR1
    174 36198_at 0.3167 0.0058 KIAA0016
    42 35125_at 0.3171 0.0540 RPS6
    1227 32438_at 0.3172 0.0557 RPS20
    236 37030_at 0.3181 0.0006 KIAA0887
    193 37703_at 0.3183 0.0011 RABGGTB
    1577 1711_at 0.3199 0.0463 TP53BP1
    461 41691_at 0.3216 0.0006 KIAA0794
    587 32079_at 0.3219 0.0037 KIAA0639
    725 39865_at 0.3230 0.0151 UNK_AI890903
    160 34326_at 0.3232 0.0025 COPB
    1157 34808_at 0.3244 0.0188 KIAA0999
    981 36129_at 0.3244 0.0014 UNK_AB007857
    50 37672_at 0.3249 0.0077 USP7
    71 32208_at 0.3257 0.0098 KIAA0355
    215 35298_at 0.3266 0.0973 EIF3S7
    290 36982_at 0.3267 0.0018 USP14
    1308 31573_at 0.3292 0.0566 RPS25
    307 36603_at 0.3292 0.0015 GCN1L1
    4 36189_at 0.3310 0.0661 ILF2
    68 39155_at 0.3325 0.0433 PSMD3
  • TABLE 9c
    Prognosis Genes Indicative of High Risk for TTD
    SEQ ID NO: HgU95A Qualifier Hazard Ratio P-Value Gene Name
    5315 40771_at 9.6763 0.0122 MSN
    5314 39811_at 8.0370 0.0149 UNK_AA402538
    5313 37298_at 7.6453 0.0021 GABARAP
    5312 38483_at 6.7764 0.0001 HSA011916
    5311 1878_g_at 6.1122 0.0004 ERCC1
    5310 33994_g_at 4.9451 0.0009 MYL6
    5309 32318_s_at 4.9169 0.0027 ACTB
    5308 37012_at 4.8396 0.0057 CAPZB
    5307 1199_at 4.7016 0.0103 EIF4A1
    5306 36641_at 4.5981 0.0042 CAPZA2
    5305 34160_at 4.5693 0.0086 ACTG1
    5304 34091_s_at 4.4114 0.0158 VIM
    5303 286_at 4.2492 0.0000 H2AFO
    5302 35770_at 4.1617 0.0083 ATP6S1
    5301 33341_at 4.0632 0.0102 GNB1
    5300 33659_at 4.0505 0.0074 CFL1
    5299 935_at 4.0159 0.0016 CAP
    5298 40134_at 3.8316 0.0043 ATP5J2
    5297 37346_at 3.8205 0.0126 ARF5
    5296 37023_at 3.8170 0.0059 LCP1
    5295 38451_at 3.8077 0.0034 UQCR
    5294 34836_at 3.7786 0.0080 RABL
    5293 35263_at 3.6729 0.0558 EIF4EBP2
    5292 41724_at 3.6595 0.0026 DXS1357E
    5291 33679_f_at 3.5643 0.0134 TUBB2
    5290 33121_g_at 3.5151 0.0007 RGS10
    5289 40872_at 3.4884 0.0013 COX6B
    5288 1315_at 3.4428 0.0026 UNK_D78361
    5287 36574_at 3.4083 0.1032 IDH3G
    5286 1131_at 3.3872 0.0002 MAP2K2
    5285 31444_s_at 3.3199 0.0016 ANXA2P2
    5284 36963_at 3.3124 0.0060 PGD
    5283 35083_at 3.2546 0.0517 UNK_AL031670
    5282 32145_at 3.2308 0.0012 ADD1
    AFFX- 3.1377 0.0060 BACTIN3_Hs_AFFX
    HSAC07/X00351_3_at
    5281 769_s_at 3.1358 0.0006 ANXA2
    5280 35783_at 3.0738 0.0592 UNK_H93123
    5279 32609_at 3.0361 0.0000 H2AFO
    5278 1695_at 3.0329 0.0225 NEDD8
  • TABLE 9d
    Prognosis Genes Indicative of Low Risk for TTD
    SEQ Hazard
    ID NO: HgU95A Qualifier Ratio P-Value Gene Name
    1 41606_at 0.0322 0.0000 DRG1
    2 38016_at 0.0547 0.0003 HNRPD
    3 39274_at 0.1030 0.0004 NUP62
    4 36189_at 0.1100 0.0029 ILF2
    5 35353_at 0.1140 0.0000 PSMC2
    6 1728_at 0.1250 0.0001 BMI1
    7 40252_g_at 0.1265 0.0003 HRB2
    8 36210_g_at 0.1287 0.0003 FSRG1
    9 34315_at 0.1288 0.0028 AFG3L2
    10 34647_at 0.1295 0.0001 DDX5
    11 38702_at 0.1333 0.0000 UNK_AF070640
    12 39415_at 0.1428 0.0019 HNRPK
    13 33818_at 0.1433 0.0011 UNK_AC004472
    14 37509_at 0.1447 0.0001 UNK_AF046059
    15 31952_at 0.1466 0.0025 RPL6
    16 37385_at 0.1538 0.0000 CYP
    17 33485_at 0.1591 0.0010 RPL4
    18 34695_at 0.1620 0.0013 GA17
    19 37609_at 0.1625 0.0004 NUBP1
    20 32807_at 0.1675 0.0012 DKFZP566C134
    21 33614_at 0.1694 0.0017 RPL18A
    22 32758_g_at 0.1727 0.0010 RAE1
    23 32766_at 0.1742 0.0056 G22P1
    24 36872_at 0.1763 0.0001 ARPP-19
    25 34401_at 0.1764 0.0095 UQCRFS1
    26 36186_at 0.1791 0.0047 RNPS1
    27 35319_at 0.1792 0.0000 CTCF
    28 755_at 0.1796 0.0023 ITPR1
    29 40370_f_at 0.1809 0.0104 HLA-G
    30 37353_g_at 0.1824 0.0013 SP100
    31 41295_at 0.1825 0.0005 GPX3
    32 36845_at 0.1886 0.0001 KIAA0136
    33 229_at 0.1887 0.0008 CBF2
    34 39766_r_at 0.1906 0.0016 POLR2K
    35 40426_at 0.1909 0.0183 BCL7B
    36 38456_s_at 0.1912 0.0240 UNK_AL049650
    37 35595_at 0.1945 0.0000 CGRP-RCP
    38 35656_at 0.1945 0.0001 RNF6
    39 35753_at 0.1955 0.0014 PRP8
    40 37367_at 0.1965 0.0429 ATP6E
    41 38590_r_at 0.1981 0.0171 PTMA
    42 35125_at 0.2004 0.0120 RPS6
    43 37381_g_at 0.2014 0.0003 GTF2B
    44 36946_at 0.2024 0.0004 DYRK1A
    45 38068_at 0.2027 0.0010 AMFR
    46 32175_at 0.2049 0.0156 CDC10
    47 31538_at 0.2057 0.0031 RPLP0
    48 39727_at 0.2079 0.0003 DUSP11
    49 36456_at 0.2120 0.0003 DKFZP564I052
    50 37672_at 0.2121 0.0013 USP7
    51 41288_at 0.2154 0.0060 CALM1
    52 38114_at 0.2167 0.0036 RAD21
    53 33543_s_at 0.2190 0.0002 PNN
    54 35325_at 0.2193 0.0043 UNK_AF052113
    55 39562_at 0.2197 0.0018 CGGBP1
    56 37737_at 0.2226 0.0004 PCMT1
    57 33740_at 0.2241 0.0061 UNK_AF023268
    58 1361_at 0.2250 0.0030 TERF1
    59 1020_s_at 0.2250 0.0020 SIP2-28
    60 38102_at 0.2281 0.0001 UNK_W28575
    61 35294_at 0.2308 0.0003 SSA2
    62 40700_at 0.2309 0.0022 SP140
    63 39020_at 0.2310 0.0067 SIVA
    64 1449_at 0.2311 0.0025 PSMA4
    65 34821_at 0.2319 0.0007 DKFZP586D0623
    66 36783_f_at 0.2319 0.0010 H-PLK
    67 39740_g_at 0.2329 0.0085 NACA
    68 39155_at 0.2333 0.0138 PSMD3
    69 39864_at 0.2344 0.0002 CIRBP
    70 39099_at 0.2361 0.0011 SEC23A
    71 32208_at 0.2365 0.0036 KIAA0355
    72 39027_at 0.2377 0.0174 COX4
    73 39774_at 0.2390 0.0207 OXA1L
    74 40449_at 0.2391 0.0006 RFC1
    75 40369_f_at 0.2395 0.0154 UNK_AL022723
    76 33151_s_at 0.2407 0.0002 UNK_W25932
    77 37625_at 0.2410 0.0000 IRF4
    78 35055_at 0.2415 0.0223 BTF3
    79 33845_at 0.2416 0.0065 HNRPH1
    80 33451_s_at 0.2418 0.0128 RPL22
    81 38527_at 0.2425 0.0064 NONO
    82 40563_at 0.2425 0.0001 DKFZP564A043
    83 36975_at 0.2427 0.0037 UNK_W26659
    84 38854_at 0.2445 0.0037 KIAA0635
    85 35163_at 0.2485 0.0001 KIAA1041
    86 38817_at 0.2492 0.0087 SPAG7
    87 41787_at 0.2502 0.0004 KIAA0669
    88 649_s_at 0.2504 0.0001 CXCR4
    89 37715_at 0.2510 0.0002 SNW1
    90 33403_at 0.2511 0.0000 DKFZP547E1010
    91 34172_s_at 0.2512 0.0013 UNK_M99578
    92 32576_at 0.2522 0.0151 EIF3S5
    93 39378_at 0.2550 0.1231 BECN1
    94 35286_r_at 0.2554 0.0009 RY1
    95 37350_at 0.2559 0.0102 UNK_AL031177
    96 38123_at 0.2559 0.0025 D123
    97 41506_at 0.2559 0.0001 MAPKAPK5
    98 40140_at 0.2559 0.0004 ZFP103
    99 38073_at 0.2561 0.0018 RNMT
    100 31872_at 0.2563 0.0029 SSXT
    101 34349_at 0.2564 0.0035 SEC63L
    102 39792_at 0.2568 0.0002 HNRPR
    103 35187_at 0.2578 0.0061 UNK_AL080216
    104 1220_g_at 0.2578 0.0003 IRF2
    105 33706_at 0.2584 0.0209 SART1
    106 34809_at 0.2588 0.0102 KIAA0999
    107 39342_at 0.2588 0.0499 MARS
    108 40874_at 0.2593 0.0541 EDF1
    109 40814_at 0.2597 0.0009 IDS
    110 39809_at 0.2597 0.0000 HBP1
    111 37226_at 0.2599 0.0014 BNIP1
    112 34370_at 0.2604 0.0020 ARCN1
    113 40651_s_at 0.2604 0.0010 CRHR1
    114 40816_at 0.2607 0.0004 PWP1
    115 35195_at 0.2613 0.0051 RPC
    116 40110_at 0.2621 0.0108 IDH3B
    117 33886_at 0.2625 0.0019 SSH3BP1
    118 34879_at 0.2639 0.0015 DPM1
    119 36968_s_at 0.2660 0.0019 OIP2
    120 36303_f_at 0.2669 0.0006 ZNF85
    121 40219_at 0.2670 0.0103 HIS1
    122 38942_r_at 0.2670 0.0105 UNK_W28610
    123 32487_s_at 0.2672 0.0061 KPNA4
    124 36754_at 0.2675 0.0001 ADCYAP1
    125 39739_at 0.2683 0.0496 MYH9
    126 33443_at 0.2687 0.0004 UNK_Z99129
    127 31950_at 0.2687 0.0321 PABPC1
    128 39059_at 0.2689 0.0145 DHCR7
    129 33831_at 0.2702 0.0001 CREBBP
    130 35368_at 0.2703 0.0006 ZNF207
    131 35227_at 0.2706 0.0057 RBBP8
    132 41296_s_at 0.2713 0.0009 GPX3
    133 40596_at 0.2717 0.0047 TCOF1
    134 35910_f_at 0.2720 0.0113 MMPL1
    135 34018_at 0.2722 0.0014 COL19A1
    136 36949_at 0.2722 0.0033 CSNK1D
    137 33394_at 0.2730 0.0011 DDX19
    138 34231_at 0.2734 0.0036 UNK_AF074606
    139 32288_r_at 0.2738 0.0014 KLRC3
    140 38903_at 0.2742 0.0007 GJB5
    141 38040_at 0.2743 0.0093 SPF30
    142 39126_at 0.2749 0.0043 UNK_AL080101
    143 35321_at 0.2752 0.0034 TLK2
    144 36546_r_at 0.2755 0.0142 UNK_AB011114
    145 39746_at 0.2755 0.0000 POLR2B
    146 41256_at 0.2762 0.0054 EEF1D
    147 41789_r_at 0.2781 0.0012 KIAA0669
    148 35630_at 0.2784 0.0025 LLGL2
    149 40984_at 0.2789 0.0384 UNK_W28255
    150 35199_at 0.2789 0.0035 KIAA0982
    151 40308_at 0.2791 0.0003 UNK_AI830496
    152 40803_at 0.2793 0.0014 UNK_AL050161
    153 322_at 0.2801 0.0045 PIK3R3
    154 1885_at 0.2804 0.0008 ERCC3
    155 193_at 0.2814 0.0330 TAF2G
    156 38668_at 0.2819 0.0141 KIAA0553
    157 39730_at 0.2819 0.0088 ABL1
    158 38256_s_at 0.2821 0.0009 DKFZP564O092
    159 39290_f_at 0.2832 0.0013 DKFZP564M2423
    160 34326_at 0.2833 0.0020 COPB
    161 38923_at 0.2838 0.0075 FRG1
    162 34225_at 0.2845 0.0092 UNK_AF101434
    163 35258_f_at 0.2846 0.0023 SFRS2IP
    164 31546_at 0.2847 0.0090 RPL18
    165 37659_at 0.2855 0.0180 IMMT
    166 37717_at 0.2861 0.0090 NAGR1
    167 32592_at 0.2862 0.0215 KIAA0323
    168 35978_at 0.2871 0.0215 UNK_AF009242
    169 31330_at 0.2873 0.0243 RPS19
    170 33388_at 0.2881 0.0289 UNK_AL080223
    171 40036_at 0.2883 0.0041 MAGOH
    172 41808_at 0.2888 0.0023 UNK_AF052102
    173 1683_at 0.2891 0.0021 WIT-1
    174 36198_at 0.2895 0.0014 KIAA0016
    175 38689_at 0.2897 0.0146 DJ149A16.6
    176 39141_at 0.2904 0.0053 ABCF1
    177 32593_at 0.2904 0.0090 KIAA0084
    178 32801_at 0.2914 0.0052 KIAA0317
    179 37894_at 0.2919 0.0054 CUL2
    180 38443_at 0.2921 0.0015 UNK_U79291
    181 493_at 0.2924 0.0026 CSNK1D
    182 41569_at 0.2925 0.0022 KIAA0974
    183 38455_at 0.2928 0.0066 UNK_AL049650
    184 1660_at 0.2932 0.0010 UBE2N
    185 1981_s_at 0.2932 0.0017 MAX
    186 31879_at 0.2942 0.0014 FUBP3
    187 38612_at 0.2944 0.0011 TSPAN-3
    188 1857_at 0.2950 0.0002 MADH7
    189 39047_at 0.2957 0.0010 KIAA0156
    190 35805_at 0.2962 0.0028 DKFZP434D156
    191 160_at 0.2964 0.0027 STAM
    1627_at 0.2969 0.0101 UNK_Z25437
    192 38106_at 0.2972 0.0009 YR-29
    193 37703_at 0.2973 0.0008 RABGGTB
    194 35748_at 0.2982 0.0103 EEF1B2
    195 40086_at 0.2983 0.0016 KIAA0261
    196 40103_at 0.2985 0.0053 VIL2
    197 38122_at 0.2997 0.0008 SLC23A1
    198 32590_at 0.2999 0.0113 NCL
    199 35254_at 0.3009 0.0040 FLN29
    200 33660_at 0.3013 0.0292 RPL5
    201 34763_at 0.3015 0.0001 CSPG6
    202 39431_at 0.3016 0.0001 NPEPPS
    203 41097_at 0.3019 0.0257 TERF2
    204 32352_at 0.3022 0.0045 PNMT
    205 35743_at 0.3029 0.0183 NAR
    206 39471_at 0.3036 0.0070 M11S1
    207 41413_at 0.3044 0.0131 CLPTM1
    208 1110_at 0.3048 0.0020 TRD@
    209 34600_s_at 0.3056 0.0011 TUB
    210 38014_at 0.3059 0.0113 ADAR
    211 34215_at 0.3059 0.0131 DXYS155E
    212 1017_at 0.3067 0.0048 MSH6
    213 31851_at 0.3068 0.0000 RFP2
    214 34745_at 0.3071 0.1447 UNK_AF070570
    215 35298_at 0.3073 0.1084 EIF3S7
    216 31894_at 0.3080 0.0015 CENPC1
    217 39923_at 0.3090 0.0079 UNK_AI935420
    218 35939_s_at 0.3097 0.0023 POU4F1
    219 1240_at 0.3098 0.0003 CASP2
    220 33661_at 0.3102 0.0017 RPL5
    221 41514_s_at 0.3105 0.0039 UNK_W26628
    222 35186_at 0.3115 0.0016 PAF65B
    223 34256_at 0.3121 0.0001 SIAT9
    224 37986_at 0.3124 0.0163 EPOR
    225 40828_at 0.3136 0.0010 P85SPR
    226 40515_at 0.3137 0.0178 EIF2B2
    227 40277_at 0.3140 0.0022 KIAA1080
    228 1228_s_at 0.3143 0.0070 MGEA6
    229 39917_at 0.3146 0.0341 GCP2
    230 36111_s_at 0.3146 0.0655 SFRS2
    231 36474_at 0.3157 0.0006 KIAA0776
    232 32831_at 0.3160 0.0095 TIM17
    233 1512_at 0.3161 0.0348 DYRK1A
    234 38478_at 0.3162 0.0107 SFRS8
    235 38450_at 0.3167 0.0096 SSB
    236 37030_at 0.3170 0.0018 KIAA0887
    237 37585_at 0.3170 0.0000 SNRPA1
    238 40905_s_at 0.3174 0.0001 DKFZP566J153
    239 35431_g_at 0.3177 0.0004 MED6
    240 40054_at 0.3180 0.0043 KIAA0082
    241 1420_s_at 0.3186 0.0283 EIF4A2
    242 33307_at 0.3194 0.0073 UNK_AL022316
    243 37984_s_at 0.3204 0.0236 ARF6
    244 41601_at 0.3205 0.0015 UNK_AA142964
    245 38492_at 0.3206 0.0026 KYNU
    246 32751_at 0.3208 0.0181 UNK_AF007140
    247 38075_at 0.3211 0.0018 SYPL
    248 32508_at 0.3214 0.0008 KIAA1096
    249 38426_at 0.3220 0.0073 TAF2I
    250 35327_at 0.3230 0.0203 EIF3S3
    251 1102_s_at 0.3233 0.0037 NR3C1
    252 31463_s_at 0.3235 0.0168 UNK_AL022097
    253 31722_at 0.3236 0.0236 RPL3
    254 1009_at 0.3237 0.0110 HINT
    255 38667_at 0.3239 0.0002 UNK_AA189161
    256 36375_at 0.3244 0.0095 ODF1
    257 1793_at 0.3252 0.0049 CDC2L5
    258 41235_at 0.3256 0.1646 ATF4
    259 38816_at 0.3262 0.0006 TACC2
    260 36239_at 0.3265 0.0143 POU2AF1
    261 31951_s_at 0.3270 0.0280 PABPC1
    262 38424_at 0.3271 0.0057 KIAA0747
    263 41562_at 0.3273 0.0033 BMI1
    264 1920_s_at 0.3277 0.0055 CCNG1
    265 35175_f_at 0.3288 0.0125 EEF1A2
    266 40980_at 0.3288 0.0016 UNK_W26477
    267 40833_r_at 0.3289 0.0084 DKFZP586G011
    1151_at 0.3290 0.0176 RPL22
    268 32150_at 0.3294 0.0074 GOLGA4
    269 38105_at 0.3294 0.0104 UNK_W26521
    270 32394_s_at 0.3294 0.0249 RPL23
    271 33420_g_at 0.3297 0.0003 API5
    272 39742_at 0.3298 0.0007 TANK
    273 32854_at 0.3303 0.0074 KIAA0696
    274 41337_at 0.3311 0.0088 AES
    275 35471_g_at 0.3316 0.0113 HTR2A
    276 1796_s_at 0.3322 0.0161 BCL3
    277 32541_at 0.3323 0.0013 PPP3CC
  • In another effort, nearest-neighbor analysis was employed to identify multivariate expression patterns in PBMCs of patients that were correlated with clinical responses. This approach included nearest-neighbor-based identification of transcripts most correlated with the class distinction of interest, random permutation of the sample labels to determine the significance of the discovered gene classifiers, and evaluation of the accuracy of various predictive models containing different numbers of genes by leave-one-out cross validation.
  • In one embodiment, nearest-neighbor analysis and supervised class prediction were performed using Genecluster version 2.0 which has been described by Golub, et al., supra, and is available at www.genome.wi.mit.edu/cancer/software/genecluster2.html. For the analysis, all raw expression data were log transformed and normalized to have a mean value of zero and a variance of one. Class prediction was carried out using a k-nearest-neighbors algorithm as described in Armstrong, et al., NATURE GENETICS, 30:41-47 (2002), which is incorporated herein by reference. This algorithm assigns a test sample to a class by identifying the k-nearest samples in the training set and then choosing the most common class among these k-nearest-neighbors. See Armstrong, et al., supra. For this purpose, distances can be defined by a Euclidean metric on the basis of the expression levels of a specified number of genes.
  • FIGS. 1A-1D illustrate the comparison of short and long term survivors. The class distinction is between RCC patients who had TTD of less than 150 days (the “shorter” class) and RCC patients who had TTD of greater than 550 days (the “longer” class). The relative expression levels of the class-correlated gene (rows in FIG. 1A) were indicated for each patient (columns in FIG. 1A) according to the normalized expression level scale. FIG. 1B depicts the comparison of the signal to noise similarity metric scores (S2N, i.e., |P(g,c)|) for class-correlated genes identified in this clinical stratification relative to S2N scores for the top 1%, 5% and 50% of scores for class-correlated genes resulting from randomly permuted data sets. Examples of the genes that are significantly correlated with the shorter survival-longer survival class distinction are demonstrated in Table 10. Each gene depicted in Table 10 is a prognosis gene and can be used to assign a survival class membership to an RCC patient. Table 10 also shows the HgU95A qualifier for each gene (“Qualifier”), the rank of each gene (“Rank #”), the class within which the gene is more highly expressed (“Class”), the S2N score (“Score”), the S2N score under a random permutation analysis at the 1% significance level (“Perm 1%”), the S2N score under a random permutation analysis at the 5% significance level (“Perm 5%”), and the S2N score under a random permutation analysis at the median significance level (“Perm (user)”). The genes are ranked based on their respective S2N scores. Genes more highly expressed in PBMCs of patients in the “shorter” survival class are ranked from 1 to 29, and genes more highly expressed in PBMCs of patients in the “longer” survival class are ranked from 30 to 58.
    TABLE 10
    Genes for Predicting Shorter versus Longer Survival
    SEQ ID NO: Qualifier Gene Name Rank # Class Score Perm 1% Perm 5% Perm (user)
    59 1020_s_at SIP2-28 35 Longer 1.08 1.1401024 1.0009979 0.7793364
    1665_s_at ECGF1 12 Shorter 0.98 1.1285181 0.9662982 0.7793773
    698 1815_g_at TGFBR2 38 Longer 1.04 1.0241055 0.9226947 0.7515544
    5311 1878_g_at ERCC1 27 Shorter 0.88 0.9426583 0.881932 0.7000415
    4033 214_at MSX1 1 Shorter 1.07 1.6155937 1.4316087 1.0612979
    4871 31432_g_at FCGRT 19 Shorter 0.91 1.0264453 0.9054481 0.7332006
    5219 32166_at KIAA1027 22 Shorter 0.9 0.9880754 0.8991979 0.7198438
    4951 32193_at PLXNC1 7 Shorter 1 1.1596018 1.0244524 0.834095
    5309 32318_s_at ACTB 11 Shorter 0.98 1.1415896 0.9838351 0.7869063
    4302 32475_at UNK_AF025529 10 Shorter 0.99 1.1436108 0.9918097 0.7958006
    989 32569_at PAFAH1B1 39 Longer 1.02 1.0132701 0.9045167 0.7348747
    177 32593_at KIAA0084 50 Longer 0.91 0.9281602 0.8635805 0.6594012
    20 32807_at DKFZP566C134 47 Longer 0.92 0.9647906 0.8758416 0.6699242
    76 33151_s_at UNK_W25932 46 Longer 0.93 0.9712016 0.8771132 0.6791526
    333 33354_at UNK_AA630312 56 Longer 0.9 0.8798124 0.794554 0.6361411
    126 33443_at UNK_Z99129 44 Longer 0.94 0.9718646 0.8817559 0.6883464
    5291 33679_f_at TUBB2 24 Shorter 0.89 0.9583792 0.8932177 0.7133438
    5007 33777_at TBXAS1 29 Shorter 0.88 0.9330735 0.8570948 0.6878592
    5265 33908_at CAPN1 18 Shorter 0.93 1.0345246 0.9114115 0.7411601
    4887 34033_s_at LILRA2 6 Shorter 1.01 1.1651943 1.0473512 0.8420641
    223 34256_at SIAT9 53 Longer 0.91 0.9039352 0.7969334 0.6420804
    4992 34774_at PPT 16 Shorter 0.94 1.0374199 0.9192994 0.7528306
    357 34786_at KIAA0742 32 Longer 1.17 1.2469592 1.0692165 0.8567256
    5079 34891_at PIN 23 Shorter 0.9 0.9736318 0.8943665 0.7149921
    1278 35268_at UNK_AL050171 49 Longer 0.92 0.933529 0.8717929 0.6601154
    5128 36091_at SKAP-HOM 4 Shorter 1.05 1.3414925 1.0789346 0.8906151
    771 36231_at UNK_AC002073 31 Longer 1.17 1.2800804 1.1628039 0.890024
    1253 36403_s_at UNK_AI434146 51 Longer 0.91 0.9177859 0.8269876 0.6537137
    571 36650_at CCND2 40 Longer 1.02 1.0060078 0.8974235 0.7254431
    4885 36780_at CLU 3 Shorter 1.05 1.3704714 1.1416388 0.9158475
    5284 36963_at PGD 9 Shorter 1 1.1566645 0.9935466 0.8085569
    5308 37012_at CAPZB 21 Shorter 0.9 1.0171863 0.9049488 0.7224556
    4860 37215_at PYGL 25 Shorter 0.89 0.9504848 0.8895108 0.711156
    5125 37307_at GNAI2 15 Shorter 0.96 1.0398792 0.9262021 0.7620184
    43 37381_g_at GTF2B 57 Longer 0.89 0.8785508 0.7906994 0.6284431
    4105 37397_at PECAM1 2 Shorter 1.06 1.4123416 1.195739 0.9664123
    77 37625_at IRF4 33 Longer 1.1 1.2122538 1.0414076 0.8297089
    4694 37647_at AOAH 26 Shorter 0.89 0.9455904 0.8832746 0.704616
    4843 38397_at UNK_U09196 20 Shorter 0.9 1.0259999 0.9053201 0.7286741
    442 38462_at NDUFA5 58 Longer 0.88 0.8780158 0.7896803 0.6253915
    5238 38475_at DCTN-50 13 Shorter 0.96 1.0638589 0.9525263 0.7732195
    5312 38483_at HSA011916 8 Shorter 1 1.1577479 1.0015978 0.8165922
    757 38518_at SCML2 45 Longer 0.93 0.9717825 0.8807355 0.6834326
    924 38589_i_at PTMA 52 Longer 0.91 0.9170299 0.8153701 0.6481305
    5200 38831_f_at UNK_AF053356 5 Shorter 1.02 1.3394433 1.0626743 0.864975
    189 39047_at KIAA0156 41 Longer 1.01 1.0031965 0.8962379 0.7150707
    4971 39062_at PPGB 17 Shorter 0.94 1.0372473 0.9187932 0.7441102
    110 39809_at HBP1 36 Longer 1.05 1.0694007 0.9784921 0.7662489
    399 40610_at UNK_AI743507 42 Longer 0.99 0.9986351 0.8919035 0.7074118
    1629 40861_at KIAA0026 48 Longer 0.92 0.9440813 0.8742373 0.6670547
    5187 41045_at SECTM1 28 Shorter 0.88 0.939004 0.8613926 0.6939691
    1490 41166_at IGHM 37 Longer 1.04 1.0626456 0.9303607 0.764905
    51 41288_at CALM1 43 Longer 0.96 0.9838136 0.8910337 0.6987405
    4956 41471_at S100A9 14 Shorter 0.96 1.0545503 0.9338488 0.7635493
    755 41669_at KIAA0191 34 Longer 1.1 1.1760652 1.0059531 0.8003741
    2276 432_s_at TRA@ 55 Longer 0.9 0.8808494 0.7956162 0.6383929
    88 649_s_at CXCR4 30 Longer 1.43 1.385432 1.2324574 0.9647334
    462 760_at DYRK2 54 Longer 0.9 0.8822472 0.7956202 0.6396517
  • The genes that are significantly correlated with the shorter-longer survival class distinction were used to construct gene classifiers for predicting the survival class membership of an RCC patient. Each predictor set was evaluated by cross validation to identify the predictor set with the highest accuracy for classification of the samples. In these analyses, a 58 gene predictor set (77% accuracy) was identified as the optimal classifier, as shown in FIG. 1C. Table 10 describes these 58 genes. FIG. 1D demonstrates the cross validation results for each sample using the 58-gene predictor. A leave-one-out cross validation was performed and the prediction strengths (PS) were calculated for each sample in the analysis. For the purposes of illustration, confidence scores accompanying calls of “TTD>550 days” were assigned positive values, while prediction strengths accompanying calls of “TTD<150 days” were assigned negative values.
  • A variety of other clinically relevant stratifications were also performed and relative expression levels of the optimally-sized gene classifiers in each analysis are summarized in FIGS. 2A-2E. The relative expression levels of the genes (rows) in each classifier are indicated for each patient (columns) according to the scale of FIG. 1A. FIG. 2A shows the relative gene expression levels of a 42-gene classifier for the comparison of patients with intermediate versus poor Motzer risk classification. Genes in this classifier are described in Table 11. The baseline expression levels of these genes in PBMCs of RCC patients are predictive of a patient's classification under Motzer risk assessment. FIG. 2B shows the relative gene expression levels for an 18-gene classifier identified in the comparison of patients with progressive disease versus any other clinical response. FIG. 2C demonstrates the relative gene expression levels for a 6-gene classifier identified in the comparison of patients in the lower versus upper quartiles of time to disease progression. Genes in this classifier are illustrated in Table 12. FIG. 2D shows the relative gene expression levels for a 52-gene classifier identified in the comparison of patients in the lower versus upper quartiles of survival/time to death. Finally, FIG. 2E depicts the relative expression levels for a 12-gene classifier identified in the comparison of patients with early (time to disease progression<106 days) versus all other times to disease progression (TTP≧106 days). Genes in this classifier are described in Table 13.
    TABLE 11
    Prognosis Genes for Intermediate Versus Poor Prognosis Motzer Risk
    SEQ ID NO: Qualifier Gene Name Rank # Class Score Perm 1% Perm 5% Perm (user)
    4924 1158_s_at CALM3 23 Poor 0.66 0.8522128 0.8104463 0.6502731
    3553 31620_at TBX10 39 Poor 0.49 0.6641291 0.6259432 0.5179407
    4455 31979_at PFKFB4 27 Poor 0.62 0.7544583 0.7037743 0.584796
    794 31982_at KIAA0894 11 Intermediate 0.69 0.7164902 0.6715787 0.5530081
    5083 32153_s_at UNK_U49869 42 Poor 0.49 0.6595597 0.6149676 0.5025353
    4883 32274_r_at UNK_AF052148 35 Poor 0.53 0.6744095 0.6432421 0.5315566
    759 32530_at YWHAQ 6 Intermediate 0.74 0.7697572 0.7312037 0.5964533
    92 32576_at EIF3S5 17 Intermediate 0.67 0.6919704 0.624558 0.5205478
    464 32621_at DR1 9 Intermediate 0.72 0.7232364 0.6892603 0.5680586
    23 32766_at G22P1 18 Intermediate 0.67 0.6909188 0.6235876 0.5156429
    3833 33178_at JAG1 31 Poor 0.54 0.716195 0.6647701 0.554687
    3565 33361_at GNG3LG 38 Poor 0.51 0.6721476 0.6284547 0.5196677
    126 33443_at UNK_Z99129 10 Intermediate 0.69 0.7216778 0.680077 0.5610381
    4437 34430_at GPT 25 Poor 0.65 0.8082772 0.7274678 0.6092486
    5199 34787_at NRD1 37 Poor 0.52 0.6737965 0.6314609 0.5246186
    4515 35256_at UNK_AL096737 29 Poor 0.59 0.7415469 0.6820045 0.5739685
    4688 35299_at MKNK1 24 Poor 0.65 0.8203746 0.757703 0.6259301
    27 35319_at CTCF 8 Intermediate 0.72 0.7329379 0.7102606 0.5762622
    250 35327_at EIF3S3 12 Intermediate 0.69 0.7115967 0.671292 0.5470585
    3087 36019_at STK19 40 Poor 0.49 0.6610853 0.6217781 0.5113894
    4 36189_at ILF2 16 Intermediate 0.67 0.6935341 0.6311355 0.524226
    5017 36391_at CCNT1 32 Poor 0.53 0.6823648 0.6549823 0.548012
    4733 36956_at SLC20A2 33 Poor 0.53 0.6811736 0.6523389 0.5410793
    77 37625_at IRF4 21 Intermediate 0.65 0.6670918 0.6195184 0.5060937
    2564 38064_at LRP 41 Poor 0.49 0.6599081 0.6185175 0.5034915
    247 38075_at SYPL 2 Intermediate 0.87 0.8830003 0.8203846 0.6704754
    5073 38188_s_at MAN2A2 28 Poor 0.6 0.7427558 0.6900191 0.5792173
    5123 38233_at HOMER-3 30 Poor 0.55 0.7166691 0.6707653 0.5600951
    4710 38449_at UNK_W28931 36 Poor 0.52 0.6744089 0.635525 0.5289256
    183 38455_at UNK_AL049650 4 Intermediate 0.81 0.7940041 0.7523503 0.6209757
    36 38456_s_at UNK_AL049650 5 Intermediate 0.75 0.7851316 0.7383793 0.6078528
    5312 38483_at HSA011916 22 Poor 0.71 0.9953936 0.8946025 0.7231015
    363 38738_at SMT3H1 14 Intermediate 0.68 0.7003638 0.6569433 0.5350646
    354 39057_at KNS2 19 Intermediate 0.66 0.6841608 0.6235478 0.5114179
    2976 40071_at CYP1B1 7 Intermediate 0.73 0.7407701 0.717859 0.5875649
    1918 40122_at NSAP1 20 Intermediate 0.66 0.6713382 0.6201956 0.5080141
    5255 40130_at FSTL1 34 Poor 0.53 0.6744496 0.6458221 0.5366854
    411 40189_at SET 15 Intermediate 0.67 0.69604 0.6381373 0.5306426
    415 40494_at DEDD 13 Intermediate 0.68 0.7072377 0.6653894 0.5396373
    399 40610_at UNK_AI743507 3 Intermediate 0.82 0.8709571 0.7766898 0.6476374
    727_at OATL3 26 Poor 0.63 0.7856346 0.7178927 0.5941055
    2869 859_at CYP1B1 1 Intermediate 0.88 1.0227921 0.8774775 0.7251933
  • TABLE 12
    Prognosis Genes for Lower versus Upper Quartiles of TTP
    SEQ ID NO: Qualifier Gene Name Rank # Class Score Perm 1% Perm 5% Perm (user)
    692 32635_at KIAA1113 6 Upper 1.16 1.3744625 1.0978256 0.871069
    5007 33777_at TBXAS1 3 Lower 0.92 1.4119021 1.1079456 0.8730354
    1835 37343_at ITPR3 5 Upper 1.17 1.4312017 1.1718279 0.9049279
    4829 39593_at FGL2 2 Lower 0.95 1.4426517 1.2094518 0.9016392
    954 41634_at UNK_D87445 4 Upper 1.17 1.4784068 1.2896696 0.9924999
    5299 935_at CAP 1 Lower 0.98 1.5250124 1.2581625 0.9758878
  • TABLE 13
    Prognosis Genes for Longer (≧106 days) versus Shorter (<106 days) TTP
    SEQ ID NO: Qualifier Gene Name Rank # Class Score Perm 1% Perm 5% Perm (user)
    379 1653_at RPS3A 12 Longer 0.67 0.8055016 0.7561978 0.6425947
    1665_s_at ECGF1 1 Shorter 0.85 1.0884173 1.014112 0.8190228
    698 1815_g_at TGFBR2 9 Longer 0.7 0.9029855 0.8274894 0.6774455
    5165 31675_s_at PTENP1 2 Shorter 0.85 0.98265 0.8774547 0.7430871
    643 31993_f_at UNK_U80764 7 Longer 0.77 1.0337092 0.970009 0.7476342
    989 32569_at PAFAH1B1 11 Longer 0.7 0.8284972 0.7577868 0.647478
    200 33660_at RPL5 10 Longer 0.7 0.8362634 0.782186 0.6625283
    5220 37148_at LILRB3 4 Shorter 0.77 0.9059746 0.8105006 0.6940544
    1835 37343_at ITPR3 8 Longer 0.76 0.9370008 0.8503211 0.7099578
    4843 38397_at UNK_U09196 3 Shorter 0.84 0.961974 0.841938 0.710196
    4808 40607_at DPYSL2 5 Shorter 0.75 0.8795726 0.7939292 0.6816332
    5187 41045_at SECTM1 6 Shorter 0.74 0.8546471 0.791536 0.6672204
  • Leave-one-out cross validation using the above-described gene classifiers for the clinical stratifications of intermediate versus poor prognosis Motzer risk, early progressors (TTP<106 days) versus all other patients, lower quartile TTP versus upper quartile TTP, and short term (survival<150 days) versus long term survivors (survival>550 days) yielded 74.4%, 77.8%, 77.3% and 79% overall accuracy for class assignment, respectively. Performance characteristics of the above-described classifiers are summarized in Table 14. The accuracy, sensitivity, and specificity for class assignment under each classifier using leave-one-out cross validation are demonstrated in the table. The k-nearest-neighbors algorithm as described in Armstrong, et al., supra, was employed for all evaluations.
    TABLE 14
    Performance Characteristics of Gene Classifiers from
    Supervised Approaches
    Size of
    Optimal
    Gene Accuracy Sensitivity Specificity
    Classification Classifier (%) (%) (%)
    Motzer risk Poor vs 42 74.4 72.7 76.5
    Intermediate
    Progressive disease vs 18 66.7 22.2 78.7
    any clinical response
    Lowest quartile 52 63.6 54.5 72.7
    survival vs
    highest quartile
    survival
    Lowest quartile TTP vs 6 77.3 81.8 72.7
    highest quartile TTP
    Short term survival 58 79.0 57.4 85.7
    (TTD < 150 days)
    vs long term survival
    (survival >550 days)
    Early progression 12 77.8 45.5 88.2
    TTP < 106 days
    vs all other patients
  • “Sensitivity” as used herein refers to the ratio of correct positive calls over the total of true positive calls plus false negative calls. “Specificity” refers to the ratio of correct negative calls over the total of true negative calls plus false positive calls. The genes identified in FIGS. 1A and 2A-2E and Tables 10-13, or the classifiers derived therefrom, can be used to assign an RCC patient to a respective clinical class selected from Table 14.
  • In yet another approach, unsupervised clustering was employed to identify genes that are correlated with survival. One of the primary endpoints of a clinical trial or a therapeutic treatment is survival. The above-described gene classifiers do not predict short term survival with supreme sensitivity and specificity (such as over 90%, 95%, or more). This might be due to heterogeneity in PBMC expression patterns from patients binned arbitrarily into different survival categories that precludes highly accurate prediction using forced-type supervised approaches. A pharmacogenomic assay capable of identifying short-term and long-term survivors in a significant fraction of the intended treatment population would still have obvious benefit, in terms of clinical prognosis. In an attempt to identify a more limited subset of patients with similar clinical outcomes for which class assignment would be more robust, an unsupervised hierarchical clustering approach using all genes passing the initial criteria (5,424 genes total) was employed.
  • The unsupervised hierarchical clustering was performed according to the procedure described in Eisen, et al., PROC NATL ACAD SCI U.S.A., 95:14863-14868 (1998). For hierarchical clustering, data were log transformed and normalized to have a mean value of zero and a variance of one. Hierarchical clustering results were generated using average linkage clustering and an uncentered correlation similarity metric.
  • The dendrogram in FIG. 3A shows that sample relationships grouped the RCC PBMCs (n=45) into four roughly equivalent sized subclusters designated A through D. The majority of patients in cluster A possessed significantly shorter survival than the majority of patients in cluster C, suggesting that expression differences in these two subclusters of patients could be predictive of survival in the majority of patients in these subpopulations. RCC patient PBMC expression profiles in the poor prognosis cluster (“A”) are indicated by the box around subcluster “A” in which 9 out of 12 patients exhibited survival of less than 365 days. RCC patient PBMC expression profiles in the good prognosis cluster (“C”) are indicated by the box around subcluster “C” in which 10 out of 12 patients exhibited survival of 365 or more days. In addition, prognostic Motzer scores were distinct between subclusters A and C, as indicated in FIG. 3A.
  • FIG. 3B shows the baseline expression patterns of a group of selected genes in subclusters A-D. Elevated or decreased expression values relative to the average expression value across all experiments are indicated according to the scale of FIG. 1A.
  • Kaplan-Meier analysis demonstrated that patients in the four subclusters possessed significant differences in survival (p=0.021, Wilcoxon test). Kaplan-Meier analysis showed that prognosis by PBMC gene expression signature in subgroups A (“Poor signature”) and C (“Good Signature”) yielded more significant differences in survival (p=0.0025, Wilcoxon test) than prognosis by the Motzer risk assessment (p=0.0125, Wilcoxon test). See FIG. 4A and FIG. 4B.
  • The above finding suggests that there exist biologically distinct differences in expression patterns of PBMCs that are predictive of survival in patients with RCC. Because it was possible that the observed differences in expression were driven by differences in patient demographics or even by technical differences in the samples, technical and demographical characteristics between these two subclusters (cluster “A” versus cluster “C”) were compared in Table 15 Comparison of technical and demographic parameters indicated no significant difference between these subgroups of patients, and the only significant differences between these groups appear to be the prognostic Motzer risk classification and the primary clinical endpoint of survival. Values for the individual parameters associated with profiles in each of the clusters were tested for differences (p-value).
    TABLE 15
    Significance Testing of Technical, Demographic, Prognostic and
    Clinical Parameters Observed in Patients and PBMC profiles in Good
    versus Poor Prognosis Clusters
    Poor Prognosis Good Prognosis
    Parameter (Cluster “A”) (Cluster “C”) p-value
    Technical
    Raw Q 2.34 2.45 0.5200
    GAPDH 5′/3′ ratio 0.95 0.93 0.6600
    Scale factor 2.94 2.69 0.5800
    Average frequency 16.8 19.6 0.2000
    (ppm)
    Present calls 4178 4194 0.9400
    Demographical
    Sex 9 male/3 female 9 male/3 female 1.000
    Age (years) 59.3 53.8 0.0870
    Ethnicity 100% Caucasian 100% Caucasian 1.000
    Prognostic
    assessment
    Motzer
    8 poor, 4 3 poor, 7 N/A
    classification intermediate intermediate, 2
    favorable
    Clinical endpoint
    Median survival 281 573 0.0025
    time (days)
    Average TTP (days) 117 240 0.1812b
  • Given the robust differences in median survival times between PBMC profiles in the poor and good prognosis clusters, a nearest-neighbor algorithm was employed to identify the transcripts in the subsets of PBMCs that are significantly correlated with good and poor prognosis signatures. The relative expression levels of an optimally-sized gene classifier derived from this analysis are shown in FIG. 5A. The gene classifier was composed of 158 genes. Because the good prognosis and poor prognosis clusters were identified based upon their differences in gene expression, random permutation of this nearest-neighbor analyses showed the genes in the classifier to be significantly correlated as expected (p<0.01). The relative expression levels of each gene (rows) are indicated for each patient (columns) according to the scale depicted in FIG. 1A. Each gene in the classifier and its respective expression level in each class (poor versus good prognosis cluster) are summarized in Table 16.
    TABLE 16
    Prognosis Genes for Assigning Class Membership to Patients
    in the Good and Poor Prognosis Subclusters
    SEQ ID NO: Qualifier Gene Name Rank # Class Score Perm 1% Perm 5% Perm (user)
    306 1034_at TIMP3 90 Good 1.57 1.0445594 0.9665145 0.7096911
    2737 1097_s_at CCR7 155 Good 1.23 0.8934941 0.7093403 0.5209759
    4924 1158_s_at CALM3 71 Poor 0.98 1.0384812 0.7927625 0.5121112
    1485 1267_at PRKCH 104 Good 1.46 0.9849667 0.8875619 0.6371682
    5288 1315_at UNK_D78361 11 Poor 1.51 1.1908811 0.9882026 0.6823562
    5152 1323_at UNK_X04803 76 Poor 0.96 1.0239922 0.7720025 0.5026828
    5002 1424_s_at YWHAH 8 Poor 1.56 1.2260145 0.9882028 0.712902
    2253 1479_g_at ITK 158 Good 1.22 0.8877654 0.7093402 0.5143056
    987 1717_s_at API2 85 Good 1.68 1.1154871 1.0003265 0.7644543
    1179 202_at HSF2 103 Good 1.5 0.9849667 0.900169 0.6398714
    5124 2069_s_at CTNNA1 9 Poor 1.55 1.205555 0.9882026 0.7047761
    4681 2085_s_at CTNNA1 40 Poor 1.16 1.1177368 0.8824167 0.5698908
    4231 2090_i_at UNK_H12458 62 Poor 1.01 1.0607328 0.8190967 0.525894
    4988 268_at PECAM1 34 Poor 1.25 1.1177368 0.9106545 0.5847529
    5064 283_at UQCRC1 27 Poor 1.32 1.1177368 0.9440462 0.6078221
    5303 286_at H2AFO 55 Poor 1.06 1.07645 0.8355755 0.534318
    4239 307_at ALOX5 75 Poor 0.96 1.0283809 0.7769105 0.506168
    5285 31444_s_at ANXA2P2 2 Poor 1.67 1.3424762 1.1425713 0.8610321
    5261 31504_at HDLBP 54 Poor 1.07 1.0793227 0.8362562 0.5385964
    4398 31682_s_at CSPG2 20 Poor 1.35 1.1213673 0.9803211 0.6337798
    1232 32087_at HSF2 146 Good 1.26 0.9003578 0.7252433 0.5342414
    2181 32097_at PCNT 107 Good 1.44 0.9849666 0.8821047 0.6232104
    5083 32153_s_at UNK_U49869 46 Poor 1.13 1.1102691 0.8593918 0.5556471
    603 32183_at SFRS11 108 Good 1.43 0.9849666 0.8821047 0.6206105
    277 32541_at PPP3CC 93 Good 1.56 1.0293367 0.9353749 0.6922912
    393 32680_at KIAA0551 157 Good 1.22 0.8893883 0.7093402 0.5186095
    5270 32749_s_at FLNA 61 Poor 1.02 1.0607328 0.8224345 0.5291181
    3956 32775_r_at PLSCR1 78 Poor 0.95 1.0217315 0.7712451 0.4984867
    5009 32800_at RXRA 79 Poor 0.95 1.0212312 0.7709695 0.4976646
    638 32804_at UNK_AF091263 142 Good 1.27 0.9081621 0.7369459 0.5426338
    5004 32806_at BZRP 53 Poor 1.08 1.0906383 0.8376178 0.5398285
    1331 33134_at ADCY3 101 Good 1.52 1.0293367 0.9001691 0.6478866
    1061 33267_at UNK_AF035315 140 Good 1.28 0.9149016 0.7390382 0.5443108
    5041 33371_s_at RAB31 31 Poor 1.28 1.1177368 0.9281045 0.5929822
    1715 33521_at ATP4A 111 Good 1.42 0.9608656 0.8507274 0.6137387
    5300 33659_at CFL1 77 Poor 0.96 1.0239921 0.7719817 0.5007594
    4589 33733_at ABCG2 67 Poor 0.99 1.054551 0.7991308 0.517656
    5007 33777_at TBXAS1 50 Poor 1.11 1.0997332 0.843028 0.5445145
    895 33788_at LAP70 94 Good 1.55 1.0293367 0.9353749 0.685765
    1040 33797_at MPHOSPH10 127 Good 1.33 0.9353749 0.7733641 0.571226
    1231 33819_at LDHB 97 Good 1.54 1.0293367 0.9353749 0.674343
    374 33847_s_at UNK_AI304854 125 Good 1.34 0.9353749 0.804844 0.5768012
    5262 33956_at MD-2 3 Poor 1.62 1.2851958 1.1000433 0.8143725
    4887 34033_s_at LILRA2 49 Poor 1.11 1.1055416 0.8472178 0.5492646
    223 34256_at SIAT9 133 Good 1.31 0.9240009 0.7478784 0.5555079
    4729 34268_at GAIP 52 Poor 1.1 1.0969372 0.840719 0.5409537
    4709 34311_at GLRX 66 Poor 0.99 1.0546845 0.8039182 0.52042
    5195 34400_at QP-C 72 Poor 0.98 1.0359778 0.7868937 0.5083646
    1035 34654_at MTMR1 100 Good 1.53 1.0293367 0.9353749 0.6529696
    4652 34660_at RNASE6 29 Poor 1.3 1.1177368 0.9303353 0.5994623
    3748 34665_g_at FCGR2B 4 Poor 1.6 1.2845235 1.0609695 0.7795188
    4579 34768_at DKFZP564E1962 26 Poor 1.32 1.1177368 0.9440462 0.6101461
    5199 34787_at NRD1 37 Poor 1.18 1.1177368 0.8910962 0.5777738
    303 34829_at DKC1 115 Good 1.41 0.9353749 0.8407055 0.601603
    1805 34983_at CYP26A1 147 Good 1.26 0.9001691 0.7248857 0.531943
    763 35238_at TRAF5 92 Good 1.56 1.0293367 0.9353749 0.6963615
    94 35286_r_at RY1 135 Good 1.29 0.9199694 0.7444252 0.5536141
    27 35319_at CTCF 89 Good 1.61 1.047387 0.9665145 0.7147587
    194 35748_at EEF1B2 141 Good 1.28 0.9107076 0.7378222 0.5433901
    39 35753_at PRP8 80 Good 1.79 1.2117286 1.1793184 0.9261844
    4316 35773_i_at NDUFB7 38 Poor 1.17 1.1177368 0.8840246 0.574061
    1275 35802_at KIAA1014 114 Good 1.41 0.9515032 0.8442041 0.6024917
    5230 35810_at ARPC3 13 Poor 1.49 1.185541 0.9882026 0.677634
    3081 35853_at PRKCABP 126 Good 1.34 0.9353749 0.7811259 0.5762339
    4826 35869_at MD-1 22 Poor 1.34 1.1197696 0.9543627 0.6252207
    3136 36021_at UNK_AL049409 131 Good 1.31 0.9256013 0.7528632 0.560786
    2558 36094_at TNNT3 154 Good 1.23 0.8941191 0.7129431 0.5212274
    5181 36130_f_at MT1E 69 Poor 0.98 1.0426595 0.7957169 0.5151819
    682 36155_at KIAA0275 134 Good 1.31 0.9219777 0.7474341 0.5539118
    5272 36199_at DAP 32 Poor 1.27 1.1177368 0.9266225 0.5910927
    771 36231_at UNK_AC002073 102 Good 1.51 0.9849667 0.900169 0.6418348
    1253 36403_s_at UNK_AI434146 87 Good 1.65 1.0968254 0.9748203 0.735724
    49 36456_at DKFZP4564I052 105 Good 1.45 0.9849667 0.8821048 0.6290045
    4836 36488_at EGFL5 45 Poor 1.14 1.1102691 0.8690057 0.5559479
    2214 36545_s_at UNK_AB011114 153 Good 1.24 0.894684 0.7135342 0.5253994
    5264 36675_r_at PFN1 43 Poor 1.16 1.1110159 0.8790239 0.5610438
    5268 36753_at LILRB4 64 Poor 1 1.0607327 0.8089606 0.5225678
    4885 36780_at CLU 41 Poor 1.16 1.1177368 0.8801252 0.5655208
    446 36786_at UNK_AL022721 148 Good 1.25 0.9001691 0.7246513 0.5306757
    4926 36889_at FCER1G 16 Poor 1.4 1.1736697 0.9882026 0.6554383
    136 36949_at CSNK1D 128 Good 1.33 0.9343908 0.7698004 0.5710414
    5284 36963_at PGD 63 Poor 1 1.0607327 0.8144836 0.5233427
    652 37005_at NBL1 123 Good 1.35 0.9353749 0.8079842 0.58034
    5053 37021_at CTSH 12 Poor 1.5 1.1857843 0.9882026 0.6823562
    820 37078_at CD3Z 109 Good 1.43 0.9660364 0.8821047 0.6199971
    5220 37148_at LILRB3 5 Poor 1.59 1.2723099 1.0463293 0.766221
    5116 37220_at FCGR1A 6 Poor 1.58 1.2682304 1.0439228 0.7437066
    5185 37311_at TALDO1 24 Poor 1.33 1.1197696 0.9471594 0.6192882
    1835 37343_at ITPR3 143 Good 1.27 0.908162 0.7334376 0.5423645
    2386 37462_i_at SF3A2 144 Good 1.27 0.9061325 0.732057 0.5407514
    4694 37647_at AOAH 48 Poor 1.11 1.1081125 0.8492031 0.5507001
    3961 37689_s_at FCGR2A 33 Poor 1.26 1.1177368 0.9106545 0.5880215
    714 37727_i_at RCN2 86 Good 1.67 1.1081127 0.994302 0.7482241
    578 38019_at CSNK1E 95 Good 1.55 1.0293367 0.9353749 0.6819632
    1604 38030_at KIAA0332 124 Good 1.34 0.9353749 0.8055808 0.5792956
    5085 38081_at LTA4H 10 Poor 1.54 1.1932396 0.9882026 0.6909306
    5010 38111_at CSPG2 21 Poor 1.34 1.1197697 0.9688478 0.6295477
    4828 38112_g_at CSPG2 14 Poor 1.46 1.180172 0.9882026 0.6708109
    788 38113_at KIAA0796 145 Good 1.27 0.9005588 0.7278896 0.5385186
    690 38148_at CRY1 112 Good 1.42 0.9515032 0.8507274 0.6115539
    5186 38363_at TYROBP 23 Poor 1.34 1.1197696 0.9526655 0.6241006
    4984 384_at PSMB10 65 Poor 0.99 1.0564462 0.8055046 0.521621
    5312 38483_at HSA011916 47 Poor 1.12 1.1081127 0.8492386 0.5539569
    81 38527_at NONO 139 Good 1.28 0.9153488 0.7403588 0.5454356
    482 38542_at NPM1 152 Good 1.24 0.8994522 0.7153279 0.5264516
    4791 38621_at UNK_AJ012008 70 Poor 0.98 1.040839 0.7946492 0.5128855
    11 38702_at UNK_AF070640 113 Good 1.42 0.9515032 0.8507274 0.6056142
    886 38843_at HMG2L1 110 Good 1.42 0.9609948 0.851209 0.6164021
    5192 39043_at ARPC1B 42 Poor 1.16 1.1148714 0.8795826 0.5652992
    189 39047_at KIAA0156 121 Good 1.36 0.9353749 0.8101286 0.586782
    4357 39320_at CASP1 51 Poor 1.1 1.0991173 0.842422 0.5426413
    5169 39329_at ACTN1 57 Poor 1.06 1.0681722 0.829216 0.5313845
    5240 39347_at CLAPS2 39 Poor 1.17 1.1177368 0.8826484 0.5715545
    5161 39360_at SNX3 19 Poor 1.35 1.1216959 0.9803817 0.6441603
    450 39509_at UNK_AI692348 129 Good 1.33 0.9292568 0.7677588 0.5698953
    48 39727_at DUSP11 136 Good 1.29 0.9195961 0.7429254 0.5511671
    5157 39749_at PSMD4 18 Poor 1.36 1.1250532 0.9814645 0.6473147
    69 39864_at CIRBP 106 Good 1.44 0.9849667 0.8821048 0.6261963
    4745 39971_at LYL1 73 Poor 0.97 1.034686 0.782038 0.5071201
    4886 39997_at PFC 58 Poor 1.05 1.0657651 0.8253264 0.530821
    2159 40016_g_at KIAA0303 151 Good 1.24 0.9001691 0.7179127 0.5294558
    808 40048_at UNK_D43951 130 Good 1.31 0.9281045 0.7539371 0.5626611
    1261 40092_at BAZ2A 132 Good 1.31 0.9250832 0.7514259 0.558431
    121 40219_at HIS1 138 Good 1.28 0.9159876 0.741164 0.5472672
    151 40308_at UNK_AI830496 82 Good 1.72 1.1483467 1.0505675 0.8307809
    5196 40432_at UNK_AA522891 35 Poor 1.2 1.1177368 0.8967329 0.5814439
    521 40442_f_at DKFZP564M2423 98 Good 1.54 1.0293367 0.9353749 0.6680597
    1632 40511_at GATA3 118 Good 1.39 0.9353749 0.839215 0.5919577
    4808 40607_at DPYSL2 59 Poor 1.02 1.0607328 0.8238136 0.5300378
    2130 40667_at CD6 96 Good 1.54 1.0293367 0.9353749 0.6789862
    1787 40775_at ITM2A 149 Good 1.25 0.9001691 0.7227228 0.530193
    152 40803_at UNK_AL050161 150 Good 1.25 0.9001691 0.7224947 0.5295897
    279 40868_at UNK_AA442799 120 Good 1.38 0.9353749 0.8153356 0.5874232
    1608 40896_at POU2F1 156 Good 1.23 0.8902482 0.7093403 0.518687
    5187 41045_at SECTM1 30 Poor 1.28 1.1177368 0.9303353 0.5970426
    5244 41136_s_at APP 68 Poor 0.99 1.0522225 0.7964097 0.5154617
    4972 41153_f_at CTNNA1 7 Poor 1.57 1.2448796 1.0065852 0.7184531
    4911 41155_at CTNNA1 17 Poor 1.38 1.1483397 0.986167 0.6532167
    5111 41156_g_at CTNNA1 15 Poor 1.42 1.1749569 0.9882026 0.6594592
    495 41224_at KIAA0788 88 Good 1.62 1.065765 0.9665145 0.7224365
    146 41256_at EEF1D 122 Good 1.35 0.9353749 0.8079842 0.5821422
    51 41288_at CALM1 119 Good 1.39 0.9353749 0.8157417 0.5898756
    4145 41300_s_at ITM2B 56 Poor 1.06 1.0734221 0.8317348 0.5335996
    274 41337_at AES 117 Good 1.4 0.9353749 0.8396499 0.5959157
    724 41338_at AES 83 Good 1.71 1.1325878 1.0314 0.8103616
    182 41569_at KIAA0974 99 Good 1.53 1.0293367 0.9353749 0.6633855
    1748 41577_at KIAA0823 91 Good 1.57 1.0398163 0.9665145 0.7029273
    755 41669_at KIAA0191 116 Good 1.41 0.9353749 0.8399643 0.5969042
    5167 41745_at IFITM3 74 Poor 0.97 1.0346859 0.7782155 0.5068782
    5175 430_at NP 25 Poor 1.33 1.1177368 0.9440463 0.6164243
    4686 574_s_at CASP1 36 Poor 1.2 1.1177368 0.8938736 0.5782988
    1283 663_at EIF1A 137 Good 1.29 0.9186698 0.741367 0.5490503
    5281 769_s_at ANXA2 1 Poor 1.77 1.4823041 1.2688332 0.9412579
    4412 777_at GDI2 44 Poor 1.15 1.1102691 0.8734871 0.5567811
    919 840_at ZNF220 81 Good 1.77 1.1495084 1.0703588 0.8762291
    5207 880_at FKBP1A 28 Poor 1.31 1.1177368 0.9303353 0.6
    1899 906_at STAT4 84 Good 1.7 1.118592 1.0010654 0.7911333
    AFFX- BACTINM_Hs_AFFX 60 Poor 1.02 1.0607328 0.8230627 0.5292476
    HSAC07/X00351_M_at
  • Leave-one-out cross validation using the 158-gene classifier for predicting good versus poor prognosis gene signature yielded 100% overall accuracy for class assignment. However, three of the patients in the poor prognosis cluster actually possessed substantially longer survival times, and two of the patients whose PBMC profiles segregated with the good prognosis cluster actually possessed shorter survival times. To estimate the accuracy, sensitivity and specificity of this gene classifier with respect to true clinical outcome, a poor outcome was arbitrarily defined as <365 days survival and a good outcome was defined as ≧365 days. We took into account the incorrect assignment of the outlier profiles in the clusters and defined the objective of the clinical assay as the identification of patients with short (less than 1 year) survival times. Using these criteria the performance of the 158-gene classifier (by leave-one-out cross validation) demonstrated 79% overall accuracy, correctly identifying 9 of 11 patients with short survival times (less than 1 year, 82% sensitivity) and 10 of 13 patients with long term survival times (greater than 1 year, 77% specificity). See FIG. 5B. In FIG. 5B, the confidence scores were calculated for each sample in the analysis. For the purposes of illustration, prediction strengths accompanying calls of “survival≧1 year” were assigned positive values, and prediction strengths accompanying calls of “survival<1 year” were assigned negative values. Asterisks identify the false positives in this clinical assay designed to identify short survival times, and arrowheads indicate false negatives.
  • As appreciated by one of ordinary skill in the art, prognosis genes for other solid tumors can be similarly identified according to the present invention. These genes are differentially expressed in peripheral blood cells of solid tumor patients having different clinical outcomes.
  • III. Prognosis and Selection of Treatment of RCC and Other Solid Tumors
  • The prognosis genes of the present invention can be used as surrogate markers for the prognosis of solid tumors. The prognosis genes of the present invention can also be used to select optimal treatments of solid tumors. For instance, clinical outcomes of different treatments for a solid tumor can be analyzed by using peripheral blood expression profiling. Treatments with favorable prognoses are selected for patients of interest.
  • Any solid tumor, treatment, or clinical outcome can be assessed by the present invention. As described above, clinical outcome can be measured by TTP (e.g., less than or greater than a specified period), TTD (e.g., less than or greater than a specified period), progressive disease, non-progressive disease, stable disease, complete response, partial response, minor response, or a combination thereof. Clinical outcome can also be prognosticated based on clinical classifications under traditional risk assessment methods (such as Motzer risk assessment for RCC, as described in Motzer, et al., supra). In addition, non-responsiveness to a therapeutic treatment is also considered a measurable outcome.
  • To predict clinical outcome of a patient of interest, the peripheral blood expression profile of one or more prognosis genes in the patient of interest is compared to at least one reference expression profile. Any number of prognosis genes can be used. In many embodiments, the PBMC expression profiles of the prognosis genes are correlated with patient outcome under a class-based correlation metric (such as nearest-neighbor analysis) or a statistical method (such as Spearman's rank correlation or Cox proportional hazard regression model). In one example, the prognosis genes are differentially expressed in PBMCs of one class of patients as compared to another class of patients. Both classes of patients have a solid tumor, and each class of patients has a different clinical outcome. In another example, the PBMC expression level of each prognosis gene is substantially higher or substantially lower in PBMCs of one class of patients than that in another class of patients. In still another example, the prognosis genes are substantially correlated with a class distinction between two classes of patients, where the two classes of patients have the same disease as the patient of interest, and each class of patients has a different clinical outcome. In many cases, the prognosis genes are correlated with the class distinction at above the 50%, 25%, 10%, 5%, or 1% significance level under random permutation tests.
  • One or more reference expression profiles can be used. The reference expression profile(s) can be determined concurrently with the expression profile of the patient of interest. The reference expression profile(s) can also be predetermined or prerecorded in an electronic or another storage medium. In one embodiment, the reference expression profile(s) is an average expression profile of the prognosis genes in peripheral blood samples of reference patients. Any averaging algorithm can be used to prepare the reference expression profile(s). In many cases, the reference patients have the same solid tumor as the patient of interest, and the clinical outcome of the reference patients is either known or determinable. In another embodiment, the reference patients can be divided into at least two classes, each class having a different respective clinical outcome. The peripheral blood expression profile of the prognosis genes in each class of the reference patients constitutes a separate reference profile.
  • The expression profile of the patient of interest and the reference expression profile(s) can be in any form. In one embodiment, the expression profiles comprise the expression level of each prognosis gene used in the comparison. The expression levels can have absolute, normalized, or relative values. Suitable normalization procedures include, but are not limited to, those used in nucleic acid array gene expression analyses or those described in Hill, et al., GENOME BIOL, 2:research0055.1-0055.13 (2001). In one example, the expression levels are normalized such that the mean is zero and the standard deviation is one. In another example, the expression levels are normalized based on internal or external controls, as appreciated by those skilled in the art. In still another example, the expression levels are normalized against one or more control transcripts with known abundances in blood samples. In many cases, the expression profile of the patient of interest and the reference expression profile(s) are constructed using the same or comparable methodology.
  • In another embodiment, the expression profiles comprise one or more ratios between the expression levels of different prognosis genes. The expression profiles can also include other measures that are capable of representing gene expression patterns.
  • The peripheral blood samples used in the present invention can be either whole blood samples, or samples comprising enriched PBMCs. In one example, the peripheral blood samples from the reference patients comprise enriched or purified PBMCs, and the peripheral blood sample from the patient of interest is a whole blood sample. In another example, all of the peripheral blood samples employed in the analysis comprise enriched or purified PBMCs. In many cases, the peripheral blood samples are prepared from the patient of interest and the reference patients by using the same or comparable procedures.
  • Other types of blood samples can also be employed in the present invention, provided that a statistically significant correlation exists between patient outcome and the gene expression profile in these blood samples.
  • The peripheral blood samples used in the present invention can be isolated from respective patients at any disease or treatment stage, provided that the correlation between the gene expression patterns in these peripheral blood samples and clinical outcome is statistically significant. In one embodiment, clinical outcome is measured by patients' response to a therapeutic treatment, and all of the blood samples used in the analysis are isolated prior to the therapeutic treatment. The expression profiles derived from these blood samples are baseline expression profiles for the therapeutic treatment.
  • Construction of the expression profiles typically involves detection of the expression level of each prognosis gene used in the comparison. Numerous methods are available for this purpose. For instance, the expression level of a gene can be determined by measuring the level of the RNA transcript(s) of the gene. Suitable methods include, but are not limited to, quantitative RT-PCR, Northern blot, in situ hybridization, slot-blotting, nuclease protection assay, and nucleic acid array (including bead array). The expression level of a gene can also be determined by measuring the level of the polypeptide(s) encoded by the gene. Suitable methods include, but are not limited to, immunoassays (such as ELISA, RIA, FACS, or Western blot), 2-dimensional gel electrophoresis, mass spectrometry, or protein arrays.
  • In one aspect, the expression level of a prognosis gene is determined by measuring the RNA transcript level of the gene in a peripheral blood sample. RNA can be isolated from the peripheral blood sample using a variety of methods. Exemplary methods include guanidine isothiocyanate/acidic phenol method, the TRIZOL® Reagent (Invitrogen), or the Micro-FastTrack™ 2.0 or FastTrack™ 2.0 mRNA Isolation Kits (Invitrogen). The isolated RNA can be either total RNA or mRNA. The isolated RNA can be amplified to cDNA or cRNA before subsequent detection or quantitation. The amplification can be either specific or non-specific. Suitable amplification methods include, but are not limited to, reverse transcriptase PCR (RT-PCR), isothermal amplification, ligase chain reaction, and Qbeta replicase.
  • In one embodiment, the amplification protocol employs reverse transcriptase. The isolated mRNA can be reverse transcribed into cDNA using a reverse transcriptase, and a primer consisting of oligo d(T) and a sequence encoding the phage T7 promoter. The cDNA thus produced is single-stranded. The second strand of the cDNA is synthesized using a DNA polymerase, combined with an RNase to break up the DNA/RNA hybrid. After synthesis of the double-stranded cDNA, T7 RNA polymerase is added, and cRNA is then transcribed from the second strand of the doubled-stranded cDNA. The amplified cDNA or cRNA can be detected or quantitated by hybridization to labeled probes. The cDNA or cRNA can also be labeled during the amplification process and then detected or quantitated.
  • In another embodiment, quantitative RT-PCR (such as TaqMan, ABI) is used for detecting or comparing the RNA transcript level of a prognosis gene of interest. Quantitative RT-PCR involves reverse transcription (RT) of RNA to cDNA followed by relative quantitative PCR (RT-PCR).
  • In PCR, the number of molecules of the amplified target DNA increases by a factor approaching two with every cycle of the reaction until some reagent becomes limiting. Thereafter, the rate of amplification becomes increasingly diminished until there is not an increase in the amplified target between cycles. If a graph is plotted on which the cycle number is on the X axis and the log of the concentration of the amplified target DNA is on the Y axis, a curved line of characteristic shape can be formed by connecting the plotted points. Beginning with the first cycle, the slope of the line is positive and constant. This is said to be the linear portion of the curve. After some reagent becomes limiting, the slope of the line begins to decrease and eventually becomes zero. At this point the concentration of the amplified target DNA becomes asymptotic to some fixed value. This is said to be the plateau portion of the curve.
  • The concentration of the target DNA in the linear portion of the PCR is proportional to the starting concentration of the target before the PCR is begun. By determining the concentration of the PCR products of the target DNA in PCR reactions that have completed the same number of cycles and are in their linear ranges, it is possible to determine the relative concentrations of the specific target sequence in the original DNA mixture. If the DNA mixtures are cDNAs synthesized from RNAs isolated from different tissues or cells, the relative abundances of the specific mRNA from which the target sequence was derived may be determined for the respective tissues or cells. This direct proportionality between the concentration of the PCR products and the relative mRNA abundances is true in the linear range portion of the PCR reaction.
  • The final concentration of the target DNA in the plateau portion of the curve is determined by the availability of reagents in the reaction mix and is independent of the original concentration of target DNA. Therefore, in one embodiment, the sampling and quantifying of the amplified PCR products are carried out when the PCR reactions are in the linear portion of their curves. In addition, relative concentrations of the amplifiable cDNAs can be normalized to some independent standard, which may be based on either internally existing RNA species or externally introduced RNA species. The abundance of a particular mRNA species may also be determined relative to the average abundance of all mRNA species in the sample.
  • In one embodiment, the PCR amplification utilizes internal PCR standards that are approximately as abundant as the target. This strategy is effective if the products of the PCR amplifications are sampled during their linear phases. If the products are sampled when the reactions are approaching the plateau phase, then the less abundant product may become relatively over-represented. Comparisons of relative abundances made for many different RNA samples, such as is the case when examining RNA samples for differential expression, may become distorted in such a way as to make differences in relative abundances of RNAs appear less than they actually are. This can be improved if the internal standard is much more abundant than the target. If the internal standard is more abundant than the target, then direct linear comparisons may be made between RNA samples.
  • A problem inherent in clinical samples is that they are of variable quantity or quality. This problem can be overcome if the RT-PCR is performed as a relative quantitative RT-PCR with an internal standard in which the internal standard is an amplifiable cDNA fragment that is larger than the target cDNA fragment and in which the abundance of the mRNA encoding the internal standard is roughly 5-100 fold higher than the mRNA encoding the target. This assay measures relative abundance, not absolute abundance of the respective mRNA species.
  • In another embodiment, the relative quantitative RT-PCR uses an external standard protocol. Under this protocol, the PCR products are sampled in the linear portion of their amplification curves. The number of PCR cycles that are optimal for sampling can be empirically determined for each target cDNA fragment. In addition, the reverse transcriptase products of each RNA population isolated from the various samples can be normalized for equal concentrations of amplifiable cDNAs. While empirical determination of the linear range of the amplification curve and normalization of cDNA preparations are tedious and time-consuming processes, the resulting RT-PCR assays may, in certain cases, be superior to those derived from a relative quantitative RT-PCR with an internal standard.
  • In yet another embodiment, nucleic acid arrays (including bead arrays) are used for detecting or comparing the expression profiles of a prognosis gene of interest. The nucleic acid arrays can be commercial oligonucleotide or cDNA arrays. They can also be custom arrays comprising concentrated probes for the prognosis genes of the present invention. In many examples, at least 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, or more of the total probes on a custom array of the present invention are probes for solid tumor prognosis genes. These probes can hybridize under stringent or nucleic acid array hybridization conditions to the RNA transcripts, or the complements thereof, of the corresponding prognosis genes.
  • As used herein, “stringent conditions” are at least as stringent as, for example, conditions G-L shown in Table 17. “Highly stringent conditions” are at least as stringent as conditions A-F shown in Table 17. As used in Table 1, hybridization is carried out under the hybridization conditions (Hybridization Temperature and Buffer) for about four hours, followed by two 20-minute washes under the corresponding wash conditions (Wash Temp. and Buffer).
    TABLE 17
    Stringency Conditions
    Stringency Polynucleotide Hybrid Hybridization Wash Temp.
    Condition Hybrid Length (bp)1 Temperature and BufferH and BufferH
    A DNA:DNA >50 65° C.; 1xSSC -or- 65° C.; 0.3xSSC
    42° C.; 1xSSC, 50% formamide
    B DNA:DNA <50 TB*; 1xSSC TB*; 1xSSC
    C DNA:RNA >50 67° C.; 1xSSC -or- 67° C.; 0.3xSSC
    45° C.; 1xSSC, 50% formamide
    D DNA:RNA <50 TD*; 1xSSC TD*; 1xSSC
    E RNA:RNA >50 70° C.; 1xSSC -or- 70° C.; 0.3xSSC
    50° C.; 1xSSC, 50% formamide
    F RNA:RNA <50 TF*; 1xSSC Tf*; 1xSSC
    G DNA:DNA >50 65° C.; 4xSSC -or- 65° C.; 1xSSC
    42° C.; 4xSSC, 50% formamide
    H DNA:DNA <50 TH*; 4xSSC TH*; 4xSSC
    I DNA:RNA >50 67° C.; 4xSSC -or- 67° C.; 1xSSC
    45° C.; 4xSSC, 50% formamide
    J DNA:RNA <50 TJ*; 4xSSC TJ*; 4xSSC
    K RNA:RNA >50 70° C.; 4xSSC -or- 67° C.; 1xSSC
    50° C.; 4xSSC, 50% formamide
    L RNA:RNA <50 TL*; 2xSSC TL*; 2xSSC

    1The hybrid length is that anticipated for the hybridized region(s) of the hybridizing polynucleotides. When hybridizing a polynucleotide to a target polynucleotide of unknown sequence, the hybrid length is assumed to be that of the hybridizing polynucleotide. When polynucleotides of known sequence are hybridized, the hybrid length can be determined by aligning the sequences of the polynucleotides and identifying the region or regions of optimal sequence complementarity.

    HSSPE (1x SSPE is 0.15M NaCl, 10 mM NaH2PO4, and 1.25 mM EDTA, pH 7.4) can be substituted for SSC (1x SSC is 0.15M NaCl and 15 mM sodium citrate) in the hybridization and wash buffers.

    TB* − TR*: The hybridization temperature for hybrids anticipated to be less than 50 base pairs in length should be 5-10° C. less than the melting temperature (Tm) of the hybrid, where Tm is determined according to the following equations. For hybrids less than 18 base pairs in length, Tm(° C.) = 2(# of A + T bases) + 4(# of G + C bases). For hybrids between 18 and 49 base pairs in length,
    # Tm(° C.) = 81.
  • In one example, a nucleic acid array of the present invention includes at least 2, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200, 250, or more different probes. Each of these probes is capable of hybridizing under stringent or nucleic acid array hybridization conditions to a different respective prognosis gene of the present invention. Multiple probes for the same prognosis gene can be used on the same nucleic acid array. The probe density on the array can be in any range. For instance, the density can be at least (or no more than) 5, 10, 25, 50, 100, 200, 300, 400, or 500, 1,000, 2,000, 3,000, 4,000, 5,000, or more probes/cm2.
  • The probes can be DNA, RNA, PNA, or a modified form thereof. The nucleotide residues in each probe can be either naturally occurring residues (such as deoxyadenylate, deoxycytidylate, deoxyguanylate, deoxythymidylate, adenylate, cytidylate, guanylate, and uridylate), or synthetically produced analogs that are capable of forming desired base-pair relationships. Examples of these analogs include, but are not limited to, aza and deaza pyrimidine analogs, aza and deaza purine analogs, and other heterocyclic base analogs, wherein one or more of the carbon and nitrogen atoms of the purine and pyrimidine rings are substituted by heteroatoms, such as oxygen, sulfur, selenium, and phosphorus. Similarly, the polynucleotide backbones of the probes can be either naturally occurring (such as through 5′ to 3′ linkage), or modified. For instance, the nucleotide units can be connected via non-typical linkage, such as 5′ to 2′ linkage, so long as the linkage does not interfere with hybridization. For another instance, peptide nucleic acids, in which the constitute bases are joined by peptide bonds rather than phosphodiester linkages, can be used.
  • The probes for the prognosis genes can be stably attached to discrete regions on the nucleic acid array. By “stably attached,” it means that a probe maintains its position relative to the attached discrete region during hybridization and signal detection. The position of each discrete region on the nucleic acid array can be either known or determinable. All of the methods known in the art can be used to make the nucleic acid arrays of the present invention.
  • In another embodiment, nuclease protection assays are used to quantitate RNA transcript levels in peripheral blood samples. There are many different versions of nuclease protection assays. The common characteristic of these nuclease protection assays is that they involve hybridization of an antisense nucleic acid with the RNA to be quantified. The resulting hybrid double-stranded molecule is then digested with a nuclease that digests single-stranded nucleic acids more efficiently than double-stranded molecules. The amount of antisense nucleic acid that survives digestion is a measure of the amount of the target RNA species to be quantified. Examples of suitable nuclease protection assays include the RNase protection assay provided by Ambion, Inc. (Austin, Tex.).
  • Hybridization probes or amplification primers for the prognosis genes of the present invention can be prepared by using any method known in the art. For prognosis genes whose genomic locations have not been determined or whose identities are solely based on EST or mRNA data, the probes/primers for these genes can be derived from the corresponding SEQ ID NOs, Entrez accession numbers, or EST or mRNA sequences.
  • In one embodiment, the probes/primers for each prognosis gene significantly diverge from the sequences of other prognosis genes. This can be achieved by checking potential probe/primer sequences against a human genome sequence database, such as the Entrez database at the NCBI. One algorithm suitable for this purpose is the BLAST algorithm. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold. The initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence to increase the cumulative alignment score. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always>0) and N (penalty score for mismatching residues; always<0). The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. These parameters can be adjusted for different purposes, as appreciated by those skilled in the art.
  • In another aspect, the expression levels of the prognosis genes of the present invention are determined by measuring the levels of polypeptides encoded by the prognosis genes. Methods suitable for this purpose include, but are not limited to, immunoassays such as ELISA, RIA, FACS, dot blot, Western Blot, immunohistochemistry, and antibody-based radioimaging. In addition, high-throughput protein sequencing, 2-dimensional SDS-polyacrylamide gel electrophoresis, mass spectrometry, or protein arrays can be used.
  • In one embodiment, ELISAs are used for detecting the levels of the target proteins. In an exemplifying ELISA, antibodies capable of binding to the target proteins are immobilized onto selected surfaces exhibiting protein affinity, such as wells in a polystyrene or polyvinylchloride microtiter plate. Samples to be tested are then added to the wells. After binding and washing to remove non-specifically bound immunocomplexes, the bound antigen(s) can be detected. Detection can be achieved by the addition of a second antibody which is specific for the target proteins and is linked to a detectable label. Detection can also be achieved by the addition of a second antibody, followed by the addition of a third antibody that has binding affinity for the second antibody, with the third antibody being linked to a detectable label. Before being added to the microtiter plate, cells in the samples can be lysed or extracted to separate the target proteins from potentially interfering substances.
  • In another exemplifying ELISA, the samples suspected of containing the target proteins are immobilized onto the well surface and then contacted with the antibodies. After binding and washing to remove non-specifically bound immunocomplexes, the bound antigen is detected. Where the initial antibodies are linked to a detectable label, the immunocomplexes can be detected directly. The immunocomplexes can also be detected using a second antibody that has binding affinity for the first antibody, with the second antibody being linked to a detectable label.
  • Another exemplary ELISA involves the use of antibody competition in the detection. In this ELISA, the target proteins are immobilized on the well surface. The labeled antibodies are added to the well, allowed to bind to the target proteins, and detected by means of their labels. The amount of the target proteins in an unknown sample is then determined by mixing the sample with the labeled antibodies before or during incubation with coated wells. The presence of the target proteins in the unknown sample acts to reduce the amount of antibody available for binding to the well and thus reduces the ultimate signal.
  • Different ELISA formats can have certain features in common, such as coating, incubating or binding, washing to remove non-specifically bound species, and detecting the bound immunocomplexes. For instance, in coating a plate with either antigen or antibody, the wells of the plate can be incubated with a solution of the antigen or antibody, either overnight or for a specified period of hours. The wells of the plate are then washed to remove incompletely adsorbed material. Any remaining available surfaces of the wells are then “coated” with a nonspecific protein that is antigenically neutral with regard to the test samples. Examples of these nonspecific proteins include bovine serum albumin (BSA), casein and solutions of milk powder. The coating allows for blocking of nonspecific adsorption sites on the immobilizing surface and thus reduces the background caused by nonspecific binding of antisera onto the surface.
  • In ELISAs, a secondary or tertiary detection means can be used. After binding of a protein or antibody to the well, coating with a non-reactive material to reduce background, and washing to remove unbound material, the immobilizing surface is contacted with the control or clinical or biological sample to be tested under conditions effective to allow immunocomplex (antigen/antibody) formation. These conditions may include, for example, diluting the antigens and antibodies with solutions such as BSA, bovine gamma globulin (BGG) and phosphate buffered saline (PBS)/Tween and incubating the antibodies and antigens at room temperature for about 1 to 4 hours or at 4° C. overnight. Detection of the immunocomplex is facilitated by using a labeled secondary binding ligand or antibody, or a secondary binding ligand or antibody in conjunction with a labeled tertiary antibody or third binding ligand.
  • Following all incubation steps in an ELISA, the contacted surface can be washed so as to remove non-complexed material. For instance, the surface may be washed with a solution such as PBS/Tween, or borate buffer. Following the formation of specific immunocomplexes between the test sample and the originally bound material, and subsequent washing, the occurrence of the amount of immunocomplexes can be determined.
  • To provide a detecting means, the second or third antibody can have an associated label to allow detection. In one embodiment, the label is an enzyme that generates color development upon incubating with an appropriate chromogenic substrate. Thus, for example, one may contact and incubate the first or second immunocomplex with a urease, glucose oxidase, alkaline phosphatase or hydrogen peroxidase-conjugated antibody for a period of time and under conditions that favor the development of further immunocomplex formation (e.g., incubation for 2 hours at room temperature in a PBS-containing solution such as PBS-Tween).
  • After incubation with the labeled antibody, and subsequent washing to remove unbound material, the amount of label can be quantified, e.g., by incubation with a chromogenic substrate such as urea and bromocresol purple or 2,2′-azido-di-(3-ethyl)-benzthiazoline-6-sulfonic acid (ABTS) and H2O2, in the case of peroxidase as the enzyme label. Quantitation can be achieved by measuring the degree of color generation, e.g., using a spectrophotometer.
  • Another method suitable for detecting polypeptide levels is RIA (radioimmunoassay). An exemplary RIA is based on the competition between radiolabeled-polypeptides and unlabeled polypeptides for binding to a limited quantity of antibodies. Suitable radiolabels include, but are not limited to, I125. In one embodiment, a fixed concentration of I125-labeled polypeptide is incubated with a series of dilution of an antibody specific to the polypeptide. When the unlabeled polypeptide is added to the system, the amount of the I125-polypeptide that binds to the antibody is decreased. A standard curve can therefore be constructed to represent the amount of antibody-bound I125-polypeptide as a function of the concentration of the unlabeled polypeptide. From this standard curve, the concentration of the polypeptide in unknown samples can be determined. Protocols for conducting RIA are well known in the art.
  • Suitable antibodies for the present invention include, but are not limited to, polyclonal antibodies, monoclonal antibodies, chimeric antibodies, humanized antibodies, single chain antibodies, Fab fragments, or fragments produced by a Fab expression library. Neutralizing antibodies (i.e., those which inhibit dimer formation) can also be used. Methods for preparing these antibodies are well known in the art. In one embodiment, the antibodies of the present invention can bind to the corresponding prognosis gene products or other desired antigens with binding affinities of at least 104 M−1, 105 M−1, 106 M−1, 107 M−1, or more.
  • The antibodies of the present invention can be labeled with one or more detectable moieties to allow for detection of antibody-antigen complexes. The detectable moieties can include compositions detectable by spectroscopic, enzymatic, photochemical, biochemical, bioelectronic, immunochemical, electrical, optical or chemical means. The detectable moieties include, but are not limited to, radioisotopes, chemiluminescent compounds, labeled binding proteins, heavy metal atoms, spectroscopic markers such as fluorescent markers and dyes, magnetic labels, linked enzymes, mass spectrometry tags, spin labels, electron transfer donors and acceptors, and the like.
  • The antibodies of the present invention can be used as probes to construct protein arrays for the detection of expression profiles of the prognosis genes. Methods for making protein arrays or biochips are well known in the art. In many embodiments, a substantial portion of probes on a protein array of the present invention are antibodies specific for the prognosis gene products. For instance, at least 10%, 20%, 30%, 40%, 50%, or more probes on the protein array can be antibodies specific for the prognosis gene products.
  • In yet another aspect, the expression levels of the prognosis genes of are determined by measuring the biological functions or activities of these genes. Where a biological function or activity of a gene is known, suitable in vitro or in vivo assays can be developed to evaluate the function or activity. These assays can be subsequently used to assess the level of expression of the prognosis gene.
  • With the expression level of each prognosis gene determined, numerous approaches can be employed to compare expression profiles. Comparison between the expression profile of a patient of interest and the reference expression profile(s) can be conducted manually or electronically. In one example, comparison is carried out by comparing each component in one expression to the corresponding component in another expression profile. The component can be the expression level of a prognosis gene, a ratio between the expression levels of two prognosis genes, or another measure capable of representing gene expression patterns. The expression level of a gene can have an absolute or a normalized or relative value. The difference between two corresponding components can be assessed by fold changes, absolute differences, or other suitable means.
  • Comparison between expression profiles can also be conducted using pattern recognition or comparison programs, such as the k-nearest-neighbors algorithm as described in Armstrong, et al., supra, or the weighted voting algorithm as described below. In addition, the serial analysis of gene expression (SAGE) technology, the GEMTOOLS gene expression analysis program (Incyte Pharmaceuticals), the GeneCalling and Quantitative Expression Analysis technology (Curagen), and other suitable methods, programs or systems can be used to compare expression profiles.
  • Multiple prognosis genes can be used in the comparison of expression profiles. For instance, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 30, 40, 50, or more prognosis genes can be used. In addition, the prognosis gene(s) used in the comparison can be selected to have relatively small p-values (e.g., two-sided p-values). In one example, the p-values indicate the statistical significance of the difference between gene expression levels in different classes of patients. In another example, the p-values suggest the statistical significance of the correlation between gene expression patterns and clinical outcome. In one embodiment, the prognosis genes used in the comparison have p-values of no greater than 0.05, 0.01, 0.001, 0.0005, 0.0001, or less. Prognosis genes with p-values of greater than 0.05 can also be used. These genes may be identified, for instance, by using a relatively small number of blood samples.
  • Similarity or difference between the expression profile of a patient of interest and the reference expression profile(s) is indicative of the class membership of the patient of interest. Similarity or difference can be determined by any suitable means.
  • In one example, a component in a reference profile is a mean value, and the corresponding component in the expression profile of the patient of interest falls within the standard deviation of the mean value. In such a case, the expression profile of the patient of interest may be considered similar to the reference profile with respect to that particular component. Other criteria, such as a multiple or fraction of the standard deviation or a certain degree of percentage increase or decrease, can be used to measure similarity.
  • In another example, at least 50% (e.g., at least 60%, 70%, 80%, 90%, or more) of the components in the expression profile of the patient of interest are considered similar to the corresponding components in a reference profile. Under these circumstances, the expression profile of the patient of interest may be considered similar to the reference profile. Different components in the expression profile may have different weights for the comparison. In some cases, lower percentage thresholds (e.g., less than 50% of the total components) are used to determine similarity.
  • The prognosis gene(s) and the similarity criteria can be selected such that the accuracy of outcome prediction (the ratio of correct calls over the total of correct and incorrect calls) is relatively high. For instance, the accuracy of prediction can be at least 50%, 60%, 70%, 80%, 90%, or more. Prognosis genes with prediction accuracy of less than 50% can also be used, provided that the prediction is statistically significant.
  • The effectiveness of outcome prediction can also be assessed by sensitivity and specificity. The prognosis genes and the comparison criteria can be selected such that both the sensitivity and specificity of outcome prediction are relatively high. For instance, the sensitivity and specificity can be at least 50%, 60%, 70%, 80%, 90%, 95%, or more. Prognosis genes having lower sensitivity or specificity can be used as long as the prediction is statistically significant.
  • Moreover, gene expression-based outcome prediction can be combined with other clinical evidence or prognostic methods to improve the effectiveness or accuracy of outcome prediction.
  • In one embodiment, the expression profile of a patient of interest is compared to at least two reference expression profiles. The first reference expression profile can be prepared from peripheral blood samples of patients in a first outcome class, and the second reference expression profile is prepared from peripheral blood samples of patients in a second outcome class. The fact that the expression profile of the patient of interest is more similar to the first reference profile than to the second reference profile suggests that the patient of interest is more likely to belong to the first outcome class, as opposed to the second outcome class.
  • Comparison between the expression profile of a patient of interest and two or more reference expression profiles can be performed by any suitable means. In one embodiment, the k-nearest-neighbors algorithm, as described in Armstrong, et al., supra, is used. The k-nearest-neighbors algorithm can effectively assign a patient to a clinical class. By “effectively,” it means that the assignment is statistically significant. For instance, the sensitivity and specificity of the assignment can be at least 50%, 60%, 70%, 80%, 90%, 95%, or more. In one example, the effectiveness of assignment is evaluated based on leave-one-out cross validation. The accuracy for leave-one-out cross validation can be, for instance, at least 50%, 60%, 70%, 80%, 90%, 95%, or more. Prognosis genes or class predictors with low assignment sensitivity/specificity or leave-one-out cross validation accuracy, such as less than 50%, can also be used in the present invention.
  • In another embodiment, a weighted voting algorithm is used. In this method, the expression level of each gene in the classifier set contributes to an overall vote on the classification of the sample. See Slonim, et al., supra. The prediction strength is a combined variable that indicates the support for one class or the other, and can vary between 0 (narrow margin of victory) and 1 (wide margin of victory) in favor of the predicted class. See Golub, et al., supra, and Slonim, et al., supra. Software programs suitable for the weight voting analysis include, but are not limited to, GeneCluster 2 software. GeneCluster 2 software is available from MIT Center for Genome Research at Whitehead Institute (e.g., www-genome.wi.mit.edu/cancer/software/genecluster2/gc2.html).
  • Under one form of the weighted voting algorithm, a set of prognosis genes are selected to create a class predictor (classifier). Each gene in the class predictor casts a weighted vote for one of the two classes (class 0 and class 1). The vote of gene “g” can be defined as vg=ag(xg−bg), wherein ag equals to P(g,c) and reflects the correlation between the expression level of gene “g” and the class distinction between the two classes, bg is calculated as bg=[x0(g)+x1(g)]/2 and represents the average of the mean logs of the expression levels of gene “g” in class 0 and class 1, and xg is the normalized log of the expression level of gene “g” in the sample of interest. A positive vg indicates a vote for class 0, and a negative vg indicates a vote for class 1. V0 denotes the sum of all positive votes, and V1 denotes the absolute value of the sum of all negative votes. A prediction strength PS is defined as PS=(V0−V1)/(V0+V1).
  • Cross-validation can be used to evaluate the accuracy of the class predictor created under the k-nearest-neighbors or weighted voting algorithm. Briefly, one sample which has been used to identify the prognosis genes under the neighborhood analysis is withheld. A class predictor is then created based on the remaining samples and used to predict the class of the sample withheld. This process can be repeated for each sample that has been used in the neighborhood analysis. Different class predictors can be evaluated using the cross-validation process, and the best class predictor with the most accurate predication can be identified.
  • Suitable prediction strength (PS) thresholds can be assessed by plotting the cumulative cross-validation error rate against the prediction strength. In one embodiment, a positive predication is made if the absolute value of PS for the sample of interest is no less than 0.3. Other PS thresholds, such as no less than 0.1, 0.2, 0.4 or 0.5, can also be used. In many embodiments, a threshold is selected such as the accuracy of prediction is optimized and the incidence of both false positive and false negative results is minimized.
  • In one example, the class predictor includes n prognosis genes identified under the neighborhood analysis. A half of these prognosis genes has the largest P(g,c) scores, and the other half has the largest −P(g,c) scores. The number n therefore is the only free parameter in defining the class predictor.
  • The prognosis genes or class predictors of the present invention can be used to assign a solid tumor patient of interest to an outcome class. In one embodiment, patients having the solid tumor can be divided into at least two classes. The first class of patients has a first specified TTD (e.g., TTD of less than 150 days from initiation of a therapeutic treatment of the solid tumor), and the second class of patients has a second specified TTD (e.g., TTD of more than 550 days from initiation of the therapeutic treatment). Genes that are substantially correlated with the class distinction between these two classes of patients can be identified and used to assign the patient of interest to one of these two outcome classes. In one example, all of the expression profiles used in the comparison are baseline profiles which are prepared from baseline peripheral blood samples isolated prior to a therapeutic treatment. In another example, the solid tumor to be prognosed is RCC, and the therapeutic treatment is a CCI-779 therapy. The prognosis gene(s) used for outcome prediction can be selected from, for instance, Table 10.
  • In another embodiment, the first class of patients has a specified TTP (e.g., TTP of no less than 106 days from initiation of a therapeutic treatment), and the second class of patients has another specified TTP (e.g., TTP of less than 106 days from initiation of the therapeutic treatment). The solid tumor can be RCC, and the therapeutic treatment can be a CCI-779 therapy. The prognosis gene(s) can be selected from, for instance, Table 13.
  • In yet another embodiment, the first class of patients includes or consists of patients having the lowest quartile of TTP among a population of patients who have the same solid tumor and are subject to the same therapeutic treatment. The second class of patients includes or consists of patients having the highest quartile of TTP among the population of patients. The solid tumor can be RCC, and the therapeutic treatment can be a CCI-779 therapy. The prognosis gene(s) can be selected from, for instance, Table 12.
  • In still yet another embodiment, the first class of patients includes or consists of patients having the lowest quartile of TTD among a population of patients who have the same solid tumor and are subject to the same therapeutic treatment, and the second class of patients includes or consists of patients having the highest quartile of TTD among the population of patients. The solid tumor can be RCC, and the therapeutic treatment can be a CCI-779 therapy.
  • In a further embodiment, the first class of patients has a prognosis determined by a risk assessment method, and the second class of patients has another prognosis determined by the same risk assessment method. In one example, both classes of patients have RCC, and the risk assessment method is based on Motzer risk classification. Under Motzer risk classification, RCC patients can have poor, intermediate, or favorable prognoses. In another example, one class of RCC patients has poor prognosis, and the other class of RCC patients has intermediate prognosis. The prognosis gene(s) can be selected from, for instance, Table 11.
  • In yet another embodiment, the first class of patients has progressive disease after a specified time of treatment, and the second class of patients has non-progressive disease (such as complete response, partial response, minor response, or stable disease) after the same specified time of treatment.
  • In still yet another embodiment, patients having the solid tumor can be clustered into at least two classes based on their gene expression profiles in PBMCs. Suitable algorithms for this purpose include, but are not limited to, unsupervised clustering analyses. Each of the two classes can be associated with a different respective clinical outcome. For instance, the majority of one class of patients can have a specified TTD (e.g., TTD of less than 365 days), while the majority of the other class of patients can have another specified TTD (e.g., TTD of no less than 365 days). Genes that are substantially correlated with the class distinction between these two classes can be identified. These genes, or the class predictors derived therefrom, can be used to predict the class membership of a patient of interest. In one example, the solid tumor is RCC, and the therapeutic treatment is a CCI-779 therapy. The prognosis gene(s) can be selected from, for instance, Table 16.
  • Prognosis genes or class predictors that are capable of distinguishing three or more different outcome classes can also be employed in the present invention. These prognosis genes can be identified using multi-class correlation metrics. Suitable programs for carrying out multi-class correlation analysis include, but are not limited to, GeneCluster 2 software (MIT Center for Genome Research at Whitehead Institute, Cambridge, Mass.). Under the analysis, patients having the solid tumor can be divided into at least three classes, and each class has a different respective clinical outcome. The prognosis genes identified under multi-class correlation analysis are differentially expressed in PBMCs of one class of patients relative to PBMCs of other classes of patients. In one embodiment, the identified prognosis genes are substantially correlated with a class distinction between the multiple classes. For instance, the prognosis genes can be selected from those above the 1%, 5%, 10%, 25%, or 50% significance level under a permutation test.
  • In accordance with another aspect of the present invention, the expression profile of the prognosis gene(s) used in the comparison is correlated with clinical outcome of reference patients under a statistical method. Suitable statistical methods for this purpose include, but are not limited to, Spearman's rank correlation, Cox proportional hazard regression model, or other rank tests or survival models. The reference patients have the same solid tumor as the patient of interest, and the clinical outcome of the reference patients is either known or determinable.
  • By comparing the expression profile of the prognosis gene(s) in a peripheral blood sample of the patient of interest to the reference expression profile of the same prognosis gene(s) in the reference patients, clinical outcome of the patient of interest can be predicted. For instance, if the expression profile of the patient of interest is more similar to the expression profile of one particular reference patient as compared to other reference patients, clinical outcome of that particular reference patient can be indicative of clinical outcome of the patient of interest.
  • Any number of prognosis genes can be used for outcome prediction based on statistical methods. In one embodiment, one prognosis gene is used. The reference patient whose expression profile is most similar to that of the patient of interest can be identified. A prediction that clinical outcome of the patient of interest is most analogous to that of the reference patient can therefore be made.
  • In another embodiment, two or more prognosis genes are used. The expression profile of the patient of interest and the reference expression profile can be compared by a pattern recognition or comparison algorithm. In one example, the Euclidean distance is used to measure the similarity between two different expression profiles.
  • Any time-associated clinical outcome indicator can be evaluated based on statistical methods. Examples of time-associated clinical outcomes include, but are not limited to, TTP and TTD.
  • In one embodiment, outcome prediction is based on Spearman's correlation test. The patient of interest and the reference patients have RCC and are being treated by a CCI-779 therapy. In one example, clinical outcome is measured by TTP, and the prognosis gene(s) is selected from Tables 6a and 6b. In another example, clinical outcome is measured by TTD, and the prognosis gene(s) is selected from Tables 6c and 6d. In yet another example, the relative risk for TTD or TTP can be qualitatively assessed based on the peripheral blood expression level of a prognosis gene in the patient of interest, in conjunction with the correlation coefficient of the prognosis gene.
  • In another embodiment, outcome prediction is based on Cox proportional hazard regression model. The patient of interest and the reference patients have RCC and are being treated by a CCI-779 therapy. In one example, clinical outcome is measured by TTP, and the prognosis gene(s) is selected from Tables 9a and 9b. In another example, clinical outcome is measured by TTD, and the prognosis gene(s) is selected from Tables 9c and 9d. In yet another example, the relative risk for TTD or TTP can be qualitatively assessed based on the peripheral blood expression level of a prognosis gene in the patient of interest, in light of the hazard ratio of the prognosis gene.
  • In yet another aspect, the present invention provides electronic systems useful for the prognosis or selection of treatment of RCC and other solid tumors. These systems include input or communication devices for receiving the expression profile of the patient of interest as well as the reference expression profile(s). The reference expression profile(s) can be stored in a database or another medium. In one embodiment, the reference expression profile(s) is readily retrievable or modifiable. The comparison between expression profiles can be conduced electronically, such as through a processor or a computer. The processor or computer can execute one or more programs to compare the expression profile of the patient of interest to the reference expression profile(s). The program(s) can be stored in a memory or downloaded from another source, such as an internet server. In one example, the program(s) includes a k-nearest-neighbors or weighted voting algorithm. In another example, the electronic system is coupled to a nucleic acid array and can receive or process expression data generated by the nucleic acid array.
  • In still another aspect, the present invention provides kits useful for the prognosis or selection of treatment of solid tumors. In one embodiment, the kits of the present invention include probes/primers for detecting expression patterns of one or more solid tumor prognosis genes. Each prognosis gene is differentially expressed in PBMCs of patients who have different clinical outcomes. In many cases, the probe/primers can hybridize under stringent or nucleic acid array hybridization conditions to the RNA transcripts, or the complements thereof, of the corresponding prognosis genes. Hybridization or amplification agents can be included in the kits.
  • The kits of the present invention can include any number of probes/primers. In one example, each kit includes at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or more different probes/primers, and each of these different probes/primers can hybridize under stringent conditions or nucleic acid array hybridization conditions to a different respective solid tumor prognosis gene. The solid tumor to be prognosed can be RCC, and the prognosis genes can be selected from Tables 6a, 6b, 6c, 6d, 9a, 9b, 9c, 9d, 10, 11, 12, 13, 16, 20 and 21.
  • In another embodiment, the kits of the present invention include one or more antibodies capable of binding to the polypeptides encoded by respective solid tumor prognosis genes. The antibodies can be, without limitation, polyclonal, monoclonal, single-chain, or humanized. In one example, the antibodies can bind to the respective polypeptide products with affinities of at least 105 M−1, 106 M−1, 107 M−1, or more. In another example, the kits of the present invention include at least 2, 3, 4, 5, 10, 15, 20, or more different antibodies, and each of these different antibodies is capable of binding to a polypeptide encoded by a different respective RCC prognosis gene. The kits of the present invention can also include immunoassay reagents, such as secondary antibodies, controls, or enzyme substrates.
  • The probes or antibodies of the present invention can be either labeled or unlabeled. Labeled antibodies can be detectable by spectroscopic, photochemical, biochemical, bioelectronic, immunochemical, electrical, optical, chemical, or other suitable means. Exemplary labeling moieties for an antibody include radioisotopes, chemiluminescent compounds, labeled binding proteins, heavy metal atoms, spectroscopic markers, such as fluorescent markers and dyes, magnetic labels, linked enzymes, mass spectrometry tags, spin labels, electron transfer donors and acceptors, and the like.
  • The probes or antibodies of the present invention can be enclosed in a vial, a tube, a bottle, a box, or another holding means. In one example, the probes or antibodies are stably attached to one or more substrate supports. Nucleic acid hybridization or immunoassays can be directly carried out on the substrate support(s). Suitable substrate supports include, but are not limited to, glasses, silica, ceramics, nylons, quartz wafers, gels, metals, papers, beads, tubes, fibers, films, membranes, column matrixes, or microtiter plate wells.
  • IV. Selection of Treatment of RCC and Other Solid Tumors
  • The present invention allows for personalized treatment of RCC or other solid tumors. Numerous treatment options or regimes can be analyzed by the present invention. Prognosis genes for each treatment can be determined. The peripheral blood expression profiles of these prognosis genes in a patient of interest can be analyzed to identify treatments that have favorable prognoses for the patient of interest. As used herein, a “favorable” prognosis is a prognosis which is better than the average prognosis for all available treatments of the solid tumor.
  • Any type of cancer treatment can be evaluated by the present invention. For instance, RCC can be treated by drug therapies. Suitable drugs include cytokines, such as interferon or interleukin 2, and chemotherapy drugs, such as CCI-779, AN-238, vinblastine, floxuridine, 5-fluorouracil, or tamoxifen. AN238 is a cytotoxic agent which has 2-pyrrolinodoxorubicin linked to a somatostatin (SST) carrier octapeptide. AN238 can be targeted to SST receptors on the surface of RCC tumor cells. Chemotherapy drugs can be used individually or in combination with other drugs, cytokines, or therapies. In addition, monoclonal antibodies, antiangiogenesis drugs, or anti-growth factor drugs can be employed to treat RCC.
  • RCC treatment can also be surgical. Suitable surgical choices include, but are not limited to, radical nephrectomy, partial nephrectomy, removal of metastases, arterial embolization, laparoscopic nephrectomy, cryoablation, and nephron-sparing surgery. Moreover, radiation, gene therapy, immunotherapy, adoptive immunotherapy, or any other conventional or experimental therapy can be used.
  • Treatment options for prostate cancer, head/neck cancer, and other solid tumors are known in the art. For instance, prostate cancer treatments include, but are not limited to, radiation therapy, hormonal therapy, and cryotherapy. The present invention contemplates any novel or experimental treatment of solid tumors.
  • Prognosis genes or class predictors for each treatment of a solid tumor can be identified according to the present invention. Treatments with favorable prognoses for a patient of interest can therefore be determined. Treatment selection can be conducted manually or electronically. In one embodiment, a reference expression profile database is established for each treatment and each prognosis gene.
  • Identification of prognosis gene may be affected by the disease stage of a solid tumor. For instance, prognosis genes can be identified from patients at a particular disease stage. Genes thus identified may be more effective in predicting clinical outcome of a patient of interest who is also at that disease stage.
  • Disease stages may also affect treatment selection. For instance, for RCC patients in stages I or II, radical or partial nephrectomy is commonly selected. For RCC patients in stage III, radical nephrectomy is among the preferred treatments. For RCC patients in stage IV, cytokine immunotherapy, combined immunotherapy and chemotherapy, or other drug therapies can be employed. Therefore, the disease stage of a patient of interest can be used to assist the gene expression-based selection for a favorable treatment of the patient.
  • It should be understood that the above-described embodiments and the following examples are given by way of illustration, not limitation. Various changes and modifications within the scope of the present invention will become apparent to those skilled in the art from the present description.
    • V. EXAMPLES Example 1 Isolation of RNA and Preparation of Labeled Microarray Targets
  • Prior to initiation of therapy, whole blood samples (8 mL) were collected into Vacutainer sodium citrate cell purification tubes (CPTs) and PBMCs were isolated according to the manufacturer's protocol (Becton Dickinson). All blood samples were shipped in CPTs overnight prior to PBMC processing. PBMCs were purified over Ficoll gradients, washed two times with PBS and counted. Total RNA was isolated from PBMC pellets using the RNeasy mini kit (Qiagen, Valencia, Calif.). Labeled target for oligonucleotide arrays was prepared using a modification of the procedure described in Lockhart, et al., NATURE BIOTECHNOLOGY, 14:1675-80 (1996). 2 μg total RNA was converted to cDNA by priming with an oligo-dT primer containing a T7 DNA polymerase promoter at the 5′ end. The cDNA was used as the template for in vitro transcription using a T7 DNA polymerase kit (Ambion, Woodlands, Tex.) and biotinylated CTP and UTP (Enzo). Labeled cRNA was fragmented in 40 mM Tris-acetate pH 8.0, 100 mM KOAc, 30 mM MgOAc for 35 minutes at 94° C. in a final volume of 40 μl.
    • Example 2 Hybridization to Affymetrix Microarrays and Detection of Fluorescence
  • Individual RCC samples were hybridized to HgU95A genechip (Affymetrix). No samples were pooled. As described above, 45 RCC patients were involved in the study. Tumors of the RCC patients were histopathologically classified as specific renal cell carcinoma subtypes using the Heidelberg classification of renal cell tumors described in Kovacs, et al., J. PATHOL., 183:131-133 (1997).
  • 10 μg of labeled target was diluted in lx MES buffer with 100 μg/ml herring sperm DNA and 50 μg/ml acetylated BSA. To normalize arrays to each other and to estimate the sensitivity of the oligonucleotide arrays, in vitro synthesized transcripts of 11 bacterial genes were included in each hybridization reaction as described in Hill, et al., SCIENCE, 290: 809-812 (2000). The abundance of these transcripts ranged from 1:300,000 (3 ppm) to 1:1000 (1000 ppm) stated in terms of the number of control transcripts per total transcripts. As determined by the signal response from these control transcripts, the sensitivity of detection of the arrays ranged between about 1:300,000 and 1:100,000 copies/million. Labeled probes were denatured at 99° C. for 5 minutes and then 45° C. for 5 minutes and hybridized to oligonucleotide arrays comprised of over 12,500 human genes (HgU95A, Affymetrix). Arrays were hybridized for 16 hours at 45° C. The hybridization buffer was comprised of 100 mM MES, 1 M [Na+], 20 mM EDTA, and 0.01% Tween 20. After hybridization, the cartridges were washed extensively with wash buffer (6×SSPET), for instance, three 10-minute washes at room temperature. These hybridization and washing conditions are collectively referred to as “nucleic acid array hybridization conditions.” The washed cartridges were then stained with phycoerythrin coupled to streptavidin.
  • 12×MES stock contains 1.22 M MES and 0.89 M [Na+]. For 1000 ml, the stock can be prepared by mixing 70.4 g MES free acid monohydrate, 193.3 g MES sodium salt and 800 ml of molecular biology grade water, and adjusting volume to 1000 ml. The pH should be between 6.5 and 6.7. 2× hybridization buffer can be prepared by mixing 8.3 ml of 12×MES stock, 17.7 mL of 5 M NaCl, 4.0 mL of 0.5 M EDTA, 0.1 mL of 10% Tween 20 and 19.9 mL of water. 6×SSPET contains 0.9 M NaCl, 60 mM NaH2PO4, 6 mM EDTA, pH 7.4, and 0.005% Triton X-100. In some cases, the wash buffer can be replaced with a more stringent wash buffer. 1000 ml stringent wash buffer can be prepared by mixing 83.3 mL of 12×MES stock, 5.2 mL of 5 M NaCl, 1.0 mL of 10% Tween 20 and 910.5 mL of water.
    • Example 3 Gene Expression Data Analysis
  • Data analysis and absent/present call determination were performed on raw fluorescent intensity values using GENECHIP 3.2 software (Affymetrix). GENECHIP 3.2 software uses algorithms to calculate the likelihood as to whether a gene is “absent” or “present” as well as a specific hybridization intensity value or “average difference” for each transcript represented on the array. For instance, “present” calls are calculated by estimating whether a transcript is detected in a sample based on the strength of the gene's signal compared to background. The algorithms used in these calculations are described in the Affymetrix GeneChip Analysis Suite User Guide (Affymetrix). The “average difference” for each transcript was normalized to “frequency” values according to the procedures of Hill, et al., SCIENCE, 290: 809-812 (2000). This was accomplished by referring the average difference values on each chip to a global calibration curve constructed from the average difference values for the 11 control transcripts with known abundance that were spiked into each hybridization solution. This calibration was used to convert average difference values for all transcripts to frequency estimates, stated in units of parts per million (ppm) ranging from about 1:300,000 (3 ppm) to 1:1000 (1000 ppm). This process also served to normalize between arrays.
  • Specific transcripts were evaluated further if they met the following criteria. First, genes that were designated “absent” by the GENECHIP 3.2 software in all samples were excluded from the analysis. Second, in comparisons of transcript levels between arrays, a gene was required to be present in at least one of the arrays. Third, for comparisons of transcript levels between groups, a Student's t-test was applied to identify a subset of transcripts that had a significant (p<0.05) differences in frequency values. In certain cases, a fourth criterion, which requires that average fold changes in frequency values across the statistically significant subset of genes be 2-fold or greater, was also used.
  • Unsupervised hierarchical clustering of genes was performed using the procedure described in Eisen, et al., supra. Nearest-neighbor prediction analysis and supervised cluster analysis was performed using metrics illustrated in Golub, et al., supra. For hierarchical clustering and nearest-neighbor prediction analysis, data were log transformed and normalized to have a mean value of zero and a variance of one. A Student's t-test was used to compare PBMC expression profiles in different outcome classes. In the comparisons, a p value<0.05 can be used to indicate statistical significance.
  • A k-nearest-neighbor's approach was used to perform a neighborhood analysis of real and randomly permuted data using a correlation metric P(g,c)=(μ1−μ2)/(σ1+σ2), where g is the expression vector of a gene, c is the class vector, μ1 and σ1 define the mean expression level and standard deviation of the gene in class 1, and μ2 and σ2 define the mean expression level and standard deviation of the gene in class 2.
    • Example 4 Gene Expression Analyses Using A More Stringent Filter
  • In this example, only those transcripts meeting a more stringent data reduction filter were used (at least 25% present calls, and an average frequency across all 45 RCC PBMCs≧5 ppm). This more stringent filter was used to avoid the inclusion low level transcripts in the predictive models. For nearest-neighbor analysis all expression data in training sets and test sets were log transformed prior to analysis. In training sets of data, models containing increasing numbers of features (transcript sequences) were built using a two-sided approach (equal numbers of features in each class) with a S2N similarity metric that used median values for the class estimate. All comparisons were binary distinctions, and each model (with increasing numbers of features) was evaluated by leave one out cross validation. Prediction of class membership in the test sets was performed using a k-nearest-neighbor algorithm in Genecluster version 2.0. In these predictions, the number of neighbors was set to k=3, the cosine distance measure used, and all k neighbors were given equal weights.
  • As demonstrated above, the Cox proportional hazards regression suggested an association between gene expression and time until disease progression, and an even stronger association between gene expression and survival. On the basis of these findings, a nearest-neighbors algorithm coupled with the stringent data reduction filter was employed to identify multivariate expression patterns in PBMCs that were correlated with and could be used to predict patient outcome. In these analyses, pretreatment expression patterns correlated with the clinical outcomes of TTP and TTD were determined.
  • In order to evaluate the predictive utility of the profiles correlated with clinical outcomes, 70% of the patient PBMC profiles were randomly selected as a training set, and the remaining 30% of the samples formed the test set. In each approach, the profiles were stratified as originating from patients with poor or favorable outcomes. A nearest-neighbors algorithm was used to generate gene classifiers correlated with groups in the training set. The gene classifier that gave the highest accuracy of class assignment by leave-one-out cross validation was identified. Finally, this gene classifier was evaluated on the test set of samples.
  • Prior to running these analyses we examined the distribution of PBMC cell types in the various groups to ensure that differences in cell populations were not the sole basis for any observed differences in expression. Tables 18 and 19 demonstrate the distributions of the various cell subtypes (neutrophils, eosinophils, lymphocytes and monocytes) between PBMCs of patients assigned to either good or poor outcome categories for TTP and survival. The mean percentages and the p-value for a t-test (unequal variance) between the good and poor outcome PBMC profiles for each cell subtype are presented. None of the cell subtypes were found to be significantly confounded with the class distinctions for either clinical outcome, ensuring that transcriptional patterns, if identified, would not simply be reflections of altered cell populations between the groups but rather distinct expression patterns arising from PBMC samples with similar cellular compositions.
    TABLE 18
    Distributions of PBMC Cell Subtypes Between PBMC Profiles
    of Patients in Good and Poor Outcome Stratifications
    of TTP in Training Set
    Cell Type TTP > 106 days TTP < 106 days p-value
    Neutrophil (%) 24.7 30.8 0.6885
    Eosinophil (%) 1.6 0.7 0.1286
    Lymphocyte (%) 47.1 37.9 0.5789
    Monocyte (%) 26.5 30.6 0.68
  • TABLE 19
    Distributions of PBMC Cell Subtypes Between PBMC Profiles
    of Patients in Good and Poor Outcome Stratifications
    of TTD in Training Set
    Cell Type TTD > 365 days TTP < 365 days p-value
    Neutrophil (%) 24.3 28.8 0.7661
    Eosinophil (%) 1.8 0.9 0.1931
    Lymphocyte (%) 48.5 40.5 0.5007
    Monocyte (%) 25.4 29.8 0.5823
  • The first analysis is summarized for the comparison of short- and long-term survivors (less than or greater than one year survival) in FIGS. 6A, 6B, and 6C. Patients were stratified as described above into two groups based upon TTD less than or greater than 365 days. A GeneCluster analysis using the signal-to-noise metric identified transcripts correlated with these groups of patients (FIG. 6A). Predictive gene classifiers containing between 2 and 60 genes in steps of 2 (and 60-200 genes in steps of 10) were evaluated by leave-one-out cross validation to identify the smallest predictive model yielding the most accurate class assignments of short- and long-term survivors in the training set. In this comparison the best model found (with respect to leave-one-out cross validation accuracy) was a classifier of 20 genes (FIG. 6B and Table 20). This predictive model was then evaluated using a nearest-neighbors approach on the remaining test set of samples (FIG. 6C). This entire approach was repeated for the stratification of short vs long-term TTP as illustrated in FIGS. 7A, 7B, and 7C. In this comparison the best model found (with respect to leave-one-out cross validation accuracy) was a classifier of 30 genes (FIG. 7B and Table 21), and this predictive model was also evaluated using a nearest-neighbors approach on the remaining test set of samples (FIG. 7C). Further detail concerning overall prediction accuracies, sensitivities and specificities of the predictive models based on year-long survival and time to progression are summarized for the test sets of samples in Table 22.
    TABLE 20
    Prognosis Genes for Short-term (<365 days) versus Long-term (>365 days) TTD
    SEQ ID NO: Qualifier Gene Name Class Score Perm 1% Perm 5% Perm (user)
    5262 33956_at MD-2 Less_365_TTD 0.63 1.1363704 0.9071798 0.66693866
    5247 41551_at RER1 Less_365_TTD 0.61 1.0375708 0.79028875 0.6129954
    5022 37009_at UNK_AL035079 Less_365_TTD 0.59 0.9283793 0.77387965 0.5757412
    3848 35300_at EPRS Less_365_TTD 0.58 0.92103595 0.74762696 0.5645757
    5008 39127_f_at PPP2R4 Less_365_TTD 0.56 0.8624204 0.70808446 0.5475367
    5161 39360_at SNX3 Less_365_TTD 0.54 0.80717504 0.6861655 0.53616226
    5054 41332_at POLR2E Less_365_TTD 0.53 0.77077115 0.67412776 0.52794206
    5092 38453_at ICAM2 Less_365_TTD 0.51 0.744897 0.6632934 0.52192914
    4914 33424_at RPN1 Less_365_TTD 0.5 0.7365122 0.64835453 0.51936203
    956_at TUBB Less_365_TTD 0.5 0.7222108 0.64653593 0.51475555
    1045 32372_at CTSB Greater_365_TTD 0.82 1.2004976 0.9564477 0.69520277
    692 32635_at KIAA1113 Greater_365_TTD 0.81 1.0586497 0.90758944 0.63466245
    1793 33493_at HFL-EDDG1 Greater_365_TTD 0.77 0.90262204 0.8435416 0.60823596
    231 36474_at KIAA0776 Greater_365_TTD 0.76 0.8723624 0.78129286 0.5796107
    1199 31864_at MPHOSPH6 Greater_365_TTD 0.75 0.84502566 0.7641664 0.56468636
    639 38317_at TCEAL1 Greater_365_TTD 0.73 0.8426697 0.7597285 0.5504346
    662 2064_g_at ERCC5 Greater_365_TTD 0.72 0.8337271 0.7298645 0.5382294
    1154 39557_at UNK_AI625844 Greater_365_TTD 0.72 0.83215594 0.699147 0.53125846
    1502 36190_at CDR2 Greater_365_TTD 0.71 0.8173296 0.6975797 0.5216159
    151 40308_at UNK_AI830496 Greater_365_TTD 0.71 0.80752265 0.6942027 0.51970375
  • TABLE 21
    Prognosis Genes for Short-term (<106 days) versus Long-term (>106 days) TTP
    Perm
    SEQ ID NO: Qualifier Gene Name Class Score Perm 1% Perm 5% (user)
    4664 181_g_at UNK_S82470 Less_TTP_106 3.41 5.582922 4.8208075 3.5752022
    4559 34498_at VNN2 Less_TTP_106 3 5.337237 4.2469945 3.2616036
    4150 38585_at HBG2 Less_TTP_106 2.95 4.1692014 3.714144 3.099498
    3984 39833_at CHRNE Less_TTP_106 2.85 4.067239 3.6665761 2.9885216
    4430 35012_at MNDA Less_TTP_106 2.84 4.032049 3.5925848 2.9256356
    4894 34946_at DORA Less_TTP_106 2.75 3.9986155 3.5583446 2.8342075
    4067 1558_g_at PAK1 Less_TTP_106 2.7 3.8789496 3.4725833 2.7667618
    4807 35820_at GM2A Less_TTP_106 2.7 3.8435366 3.4385278 2.6919303
    5244 41136_s_at APP Less_TTP_106 2.61 3.813862 3.3433113 2.6589744
    4510 32776_at RALB Less_TTP_106 2.57 3.713758 3.3420131 2.603462
    4816 34874_at NTE Less_TTP_106 2.45 3.6834376 3.3347135 2.5644205
    4509 34319_at S100P Less_TTP_106 2.35 3.598251 3.2589953 2.535933
    3860 41102_at T54 Less_TTP_106 2.31 3.5312018 3.2556353 2.4961586
    4960 32046_at PRKCD Less_TTP_106 2.28 3.5278873 3.241575 2.4784653
    4609 36960_at EDR2 Less_TTP_106 2.25 3.4799564 3.1926253 2.4267142
    2645 34871_at UNK_W30677 Greater_TTP_106 3.89 6.951508 5.112061 4.082164
    757 38518_at SCML2 Greater_TTP_106 3.67 5.105945 4.6043224 3.631336
    2290 41189_at TNFRSF12 Greater_TTP_106 3.59 5.105614 4.2503996 3.395199
    808 40048_at UNK_D43951 Greater_TTP_106 3.49 4.7581496 4.189143 3.3146112
    1733 40396_at P2RX5 Greater_TTP_106 3.49 4.513983 4.0066333 3.2069612
    1063 35177_at KIAA0725 Greater_TTP_106 3.38 4.4174356 3.9872625 3.1314178
    1619 40584_at NUP88 Greater_TTP_106 3.24 4.3745546 3.9209368 3.0728083
    1897 38340_at KIAA0655 Greater_TTP_106 3.23 4.121891 3.8479779 3.009764
    1372 37416_at ARHH Greater_TTP_106 3.22 4.105443 3.834686 2.9688578
    690 38148_at CRY1 Greater_TTP_106 3.19 4.051371 3.776217 2.9163232
    1045 32372_at CTSB Greater_TTP_106 3.18 4.0035615 3.7531464 2.8886828
    119 36968_s_at OIP2 Greater_TTP_106 3.12 3.9565299 3.6980143 2.8398302
    223 34256_at SIAT9 Greater_TTP_106 3.11 3.8674347 3.6664524 2.7820752
    1734 41767_r_at KIAA0855 Greater_TTP_106 3.1 3.8383002 3.629394 2.748495
    1253 36403_s_at UNK_AI434146 Greater_TTP_106 2.96 3.778308 3.569239 2.690984
  • TABLE 22
    Performance Characteristics of Gene Classifiers from Supervised
    Approaches for Samples in the Test Set
    Accuracy Pos Predictive Value Neg Predictive Value
    TTP 11/13 (85%) 8/10 (80%) 3/3 (100%)
    TTD 10/14 (72%)  8/8 (100%) 2/6 (33%) 
  • We identified expression patterns and individual transcript levels in pretreatment PBMC expression profiles that appear correlated with, and therefore predictive of, the clinical outcomes of time to progression and survival in patients with RCC.
  • In initial analyses, an unsupervised hierarchical clustering algorithm segregated patients solely on the basis of the similarity in their global expression profiles in PBMCs. We identified significant differences in survival between these molecularly defined subgroups of patients and, as a precautionary step, tested whether technical or demographic factors were confounded with the observed subgroups of patient PBMC profiles in good and poor outcome clusters. Key technical parameters associated with the profiles (measures of RNA quality, gene chip hybridization, etc) were not significantly different between the groups and therefore did not confound the analysis. In addition we ruled out multiple other demographic parameters (sex, age, ethnicity) as sources of the observed stratification in patient PBMC profiles. Finally, we also determined that CCI-779 dose level did not impact the observed stratifications, indicating that profiles predictive of various outcomes were not CCI-779 dose dependent.
  • The Kaplan-Meier based differences in survival curves for the subsets of patients in the good versus poor gene expression prognosis clusters were more distinct than the differences in survival for those same patients as predicted by their associated risk classifications (FIGS. 4A and 4B). This finding supports the continued exploration of surrogate tissue profiling for identification of gene expression patterns predictive of outcome, since prior to the expression profiling results in PBMCs reported here, the Motzer risk classification was the prognostic index best correlated with outcome in this clinical study.
  • Multiple supervised approaches also support the hypothesis that transcriptional levels of select genes in PBMC profiles of RCC patients are significantly correlated with disease progression and survival. Both non-parametric (Spearmans correlation, data not shown) and parametric (Cox proportional hazard modeling) univariate analyses identified individual transcripts that were significantly correlated with both disease progression and survival. Multivariate approaches using k-nearest-neighbor gene selection were also performed to identify multivariate predictors correlated with clinical outcomes of progression and survival. Supervised analyses identified gene signatures in PBMCs that were capable of identifying patients with varying accuracy with respect to TTP and survival. The overall accuracy of these predictive models on test sets of patients was 85% and 72%, respectively, and overall accuracies in both training set cross validation and in test set predictions were similar.
  • The results further imply that the circulating monocytes, T cells and B cells (or activated neutrophils passing through CPT) may serve as a sensitive monitor of the organism's physiological state. As these cells pass through various tissues, their reaction to the microenvironment is captured in a complex transcriptional response measured through profiling. Surprisingly, such patterns appear to not only be diagnostic of disease state (e.g., RCC) but may also reflect differential responses to variations in the clinically same disease state (e.g., advanced RCC with different degrees of aggressiveness). This suggests that the PBMCs, due to their transit through the body, may serve as an accessible surrogate monitor of tissues and systems that are not easily obtained by routine biopsies.
  • The functional categories of transcripts in PBMCs associated with low or high risk display several interesting trends. First, transcripts elevated in PBMCs of patients with shorter TTP or survival include those involved in cytoskeletal organization/cell motility, associated small GTPases, general pathways of proteasome-dependent catabolism and general pathways of metabolism. In contrast, transcripts elevated in PBMCs of patients with longer TTP or survival included those involved in mRNA transport, mRNA processing/splicing and ribosomal protein subunits.
  • Similar surrogate tissue analyses can be used to identify transcriptional profiles that are specific to a particular therapy in question (e.g., CCI-779, interferon-alpha (IFN-α), or CCI-779+IFN-α), as well as those that are simply prognostic of disease outcome regardless of therapy.
  • The foregoing description of the present invention provides illustration and description, but is not intended to be exhaustive or to limit the invention to the precise one disclosed. Modifications and variations are possible consistent with the above teachings or may be acquired from practice of the invention. Thus, it is noted that the scope of the invention is defined by the claims and their equivalents.

Claims (20)

1. A method comprising comparing an expression profile of at least one gene in a peripheral blood sample of a patient to at least one reference expression profile of said at least one gene, wherein the patient has a solid tumor, and each of said at least one gene is differentially expressed in peripheral blood mononuclear cells of a first class of patients as compared to peripheral blood mononuclear cells of a second class of patients, wherein both the first and second classes of patients have the solid tumor, and wherein the first class of patients has a first clinical outcome, and the second class of patients has a second clinical outcome.
2. The method according to claim 1, wherein the first and second clinical outcomes are outcomes of a therapeutic treatment of the solid tumor in the first and second classes of patients.
3. The method according to claim 2, wherein the expression profile and said at least one reference expression profile are baseline expression profiles for the therapeutic treatment.
4. The method according to claim 2, wherein the peripheral blood sample is a whole blood sample.
5. The method according to claim 2, wherein the peripheral blood sample comprises enriched peripheral blood mononuclear cells.
6. The method according to claim 2, wherein the solid tumor is RCC, and the therapeutic treatment comprises a CCI-779 therapy.
7. The method according to claim 6, wherein the first clinical outcome is TTD of less than a first specified period of time starting from initiation of the therapeutic treatment, and the second clinical outcome is TTD of longer than a second specified period of time starting from initiation of the therapeutic treatment.
8. The method according to claim 6, wherein the first clinical outcome is TTP of less than a specified period of time starting from initiation of the therapeutic treatment, and the second clinical outcome is TTP of longer than another specified period of time starting from initiation of the therapeutic treatment.
9. The method according to claim 6, wherein the first clinical outcome is a Motzer risk classification, and the second clinical outcome is another Motzer risk classification.
10. The method according to claim 2, wherein said at least one gene comprises two or more genes, and said at least one reference expression profile includes a first reference expression profile and a second reference expression profile, wherein the first reference expression profile is an average expression profile of said at least one gene in peripheral blood samples of patients selected from the first class, and the second reference expression profile is an average expression profile of said at least one gene in peripheral blood samples of patients selected from the second class, and wherein the expression profile is compared to said at least one reference expression profile by using a k-nearest-neighbors or weighted voting algorithm.
11. The method according to claim 1, wherein said at least one gene substantially correlates with a class distinction between the first class and the second class.
12. The method according to claim 1, comprising selecting a therapy for treating the solid tumor in the patient, wherein the patient has a favorable prognosis for the therapy.
13. A method comprising comparing an expression profile of at least one gene in a peripheral blood sample of a patient to at least one reference expression profile of said at least one gene, wherein the patient has a solid tumor, and each of said at least one gene is differentially expressed in peripheral blood mononuclear cells of a first class of patients as compared to peripheral blood mononuclear cells of a second class of patients, wherein the first and second classes of patients have the solid tumor, and each of the first and second classes is a subcluster formed by an unsupervised clustering analysis of gene expression profiles in peripheral blood mononuclear cells of a population of patients who have the solid tumor, and wherein the majority of the first class of patients has a first clinical outcome, and the majority of the second class of patients has a second clinical outcome.
14. The method according to claim 13, wherein the first and second clinical outcomes are outcomes of a therapeutic treatment of the solid tumor in the first and second classes of patients, and the expression profile and said at least one reference expression profile are baseline expression profiles for the therapeutic treatment.
15. The method according to claim 14, wherein the solid tumor is RCC, and the therapeutic treatment comprises a CCI-779 therapy.
16. The method according to claim 13, comprising selecting a therapy for treating the solid tumor in the patient, wherein the patient has a favorable prognosis for the therapy.
17. A method comprising comparing an expression profile of at least one gene in a peripheral blood sample of a patient to at least one reference expression profile of said at least one gene, wherein the patient has a solid tumor, and expression levels of each of said at least one gene in peripheral blood mononuclear cells of patients who have the solid tumor correlate with clinical outcomes of said patients.
18. The method according to claim 17, wherein the solid tumor is RCC, and said clinical outcomes are measured by patient response to a CCI-779 therapy, and wherein said at least one gene comprises one or more genes selected from Tables 6a, 6b, 6c, 6d, 9a, 9b, 9c, 9d, 10, 11, 12, 13, 16, 20, and 21.
19. A system comprising:
a memory or a storage medium including data that represent an expression profile of at least one gene in a peripheral blood sample of a patient who has a solid tumor;
at least another storage medium including data that represent at least one reference expression profile of said at least one gene;
a program capable of comparing the expression profile to said at least one reference expression profile; and
a processor capable of executing the program, wherein expression levels of said at least one gene in peripheral blood mononuclear cells of patients who have the solid tumor correlate with clinical outcomes of said patients.
20. A nucleic acid or protein array comprising concentrated probes for solid tumor prognosis genes, wherein each of the solid tumor prognosis genes is differentially expressed in peripheral blood mononuclear cells of a first class of patients as compared to peripheral blood mononuclear cells of a second class of patients, wherein both the first and second classes of patients have a solid tumor, and wherein the first class of patients has a first clinical outcome, and the second class of patients has a second clinical outcome.
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